DADA2 ASV table generation from 16S rRNA gene sequences of DNA from Oman samples collected in 2017
Source file: OM17_dada2_ASV_table_generation.Rmd
Daniel Nothaft
16 Jul 2020
1 Setup
Set knitting options
# global knitting options for automatic saving of all plots as .png and .pdf. Also sets cache directory.
knitr::opts_chunk$set(
dev = c("png", "pdf"), fig.keep = "all",
dev.args = list(pdf = list(encoding = "WinAnsi", useDingbats = FALSE)),
fig.path = file.path("fig_output/", paste0(gsub("\\.[Rr]md", "/", knitr::current_input()))),
cache.path = file.path("cache/", paste0(gsub("\\.[Rr]md", "/", knitr::current_input())))
)Load packages
library(dada2); packageVersion("dada2") # sequence filtering and sample inference with dada2## [1] '1.16.0'library(ShortRead); packageVersion("ShortRead") # package for loading, displaying, and handling sequences## [1] '1.46.0'library(tidyverse); packageVersion("tidyverse") # handy piping and data operations## [1] '1.3.0'library(rjson); packageVersion("rjson") # read json output from figaro## [1] '0.2.20'# source all relevant scripting files
# paths.R contains paths to local data and programs
source(file.path("scripts", "paths.R"))Set directories
# Set up names of sub directories to stay organized
preprocess_path <- file.path(project_path_OM17, "01_preprocess")
demultiplex_path <- file.path(preprocess_path, "demultiplexed")
demultiplex_assigned_path <- file.path(demultiplex_path, "assigned")
figaro_output_path <- file.path(preprocess_path, "Figaro_output")
filter_path <- file.path(project_path_OM17, "02_filter") Now we read in the names of the demultiplexed and assigned fastq files.
fnFs <- sort(list.files(demultiplex_assigned_path, pattern="_R1.fastq.gz", full.names = TRUE))
fnRs <- sort(list.files(demultiplex_assigned_path, pattern="_R2.fastq.gz", full.names = TRUE))Count and display reads for input
# count forward reads
input_read_count_F <- countLines(demultiplex_assigned_path, pattern="_R1.fastq.gz")/4
# make forward read counts into tbl with sample name
input_read_count_F_tbl <- input_read_count_F %>% as_tibble(rownames = "file_name") %>% rename(reads_F = value) %>% mutate(sample_id = sapply(strsplit(
file_name, "_R1"), `[`, 1))
# repeat for reverse
input_read_count_R <- countLines(demultiplex_assigned_path, pattern="_R2.fastq.gz")/4
input_read_count_R_tbl <- input_read_count_R %>% as_tibble(rownames = "file_name") %>% rename(reads_R = value) %>% mutate(sample_id = sapply(strsplit(
file_name, "_R2"), `[`, 1))
# Join forward and reverse together into one tbl
input_read_count_FR <- input_read_count_F_tbl %>% select(-file_name) %>% left_join(input_read_count_R_tbl %>% select(-file_name), by = "sample_id") %>% select(sample_id, everything())
# print. reads counts are same in forward and reverse, which is what we want.
input_read_count_FRPlot read counts
plot_read_count_input <- input_read_count_FR %>% ggplot(aes(
x = fct_reorder(sample_id, desc(reads_F)),
y = reads_F
)) +
geom_bar(stat = "identity") +
scale_y_continuous(name = "Forward reads") +
scale_x_discrete(name = "Sample ID") +
theme_classic(base_size = 9)+
theme(
axis.text.x = element_text(angle = 90, vjust = .5, hjust = 1),
legend.position = "bottom"
)
plot_read_count_input
Extract sample names for later use
# Extract sample names, assuming filenames have format: SAMPLENAME_XXX.fastq
sample.namesF.dots <- sapply(strsplit(basename(fnFs), "_R1"), `[`, 1)
sample.namesR.dots <- sapply(strsplit(basename(fnRs), "_R2"), `[`, 1)
# print first few names
sample.namesF.dots %>% head()## [1] "04.RNA1" "04.RNA2" "104.1" "104.2" "104.3" "104.RNA1"sample.namesR.dots %>% head()## [1] "04.RNA1" "04.RNA2" "104.1" "104.2" "104.3" "104.RNA1"2 Check primer sequences
FWD <- "CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA" # 515-Y-M13
REV <- "CCGYCAATTYMTTTRAGTTT" # 926R
(FWD_length <- str_length(FWD))## [1] 40(REV_length <- str_length(REV))## [1] 20To ensure we have the right primers, and the correct orientation of the primers on the reads, we will verify the presence and orientation of these primers in the data.
allOrients <- function(primer) {
# Create all orientations of the input sequence
require(Biostrings)
dna <- DNAString(primer) # The Biostrings works w/ DNAString objects rather than character vectors
orients <- c(Forward = dna, Complement = complement(dna), Reverse = reverse(dna),
RevComp = reverseComplement(dna))
return(sapply(orients, toString)) # Convert back to character vector
}
FWD.orients <- allOrients(FWD)
REV.orients <- allOrients(REV)
FWD.orients## Forward
## "CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA"
## Complement
## "GGCATTTTGCTGCCGGTCAGGCACRGTCGKCGGCGCCATT"
## Reverse
## "AATGGCGCCGMCGACYGTGCCTGACCGGCAGCAAAATGCC"
## RevComp
## "TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG"We are now ready to count the number of times the primers appear in the forward and reverse read, while considering all possible primer orientations. Identifying and counting the primers on one set of paired end FASTQ files is sufficient, assuming all the files were created using the same library preparation, so we’ll just process the first sample.
primerHits <- function(primer, fn) { # Counts number of reads in which the primer is found
nhits <- vcountPattern(primer, sread(readFastq(fn)), fixed = FALSE)
return(sum(nhits > 0))
}
rbind(FWD.ForwardReads = sapply(FWD.orients, primerHits, fn=fnFs[[1]]),
FWD.ReverseReads = sapply(FWD.orients, primerHits, fn=fnRs[[1]]),
REV.ForwardReads = sapply(REV.orients, primerHits, fn=fnFs[[1]]),
REV.ReverseReads = sapply(REV.orients, primerHits, fn=fnRs[[1]]))## Forward Complement Reverse RevComp
## FWD.ForwardReads 7137 0 0 0
## FWD.ReverseReads 0 0 0 551
## REV.ForwardReads 1 0 0 24
## REV.ReverseReads 5988 0 0 7As expected, the FWD primer is found in the forward reads in its forward orientation, and in the reverse reads in its reverse-complement orientation. Similarly, the REV primer is found with its expected orientations. We will remove the primers later when we truncate lower quality reads. So now let’s inspect read quality profiles.
3 Inspect read quality profiles
It’s important to get a feel for the quality of the data that we are using. To do this, we will plot the quality of some of the samples.
From the dada2 tutorial: >In gray-scale is a heat map of the frequency of each quality score at each base position. The median quality score at each position is shown by the green line, and the quartiles of the quality score distribution by the orange lines. The red line shows the scaled proportion of reads that extend to at least that position (this is more useful for other sequencing technologies, as Illumina reads are typically all the same lenghth, hence the flat red line).
# Forward reads
# If the number of samples is 20 or less, plot them all, otherwise, just plot 20 randomly selected samples
if( length(fnFs) <= 20) {
plotQualityProfile(fnFs)
} else {
rand_samples <- sample(size = 20, 1:length(fnFs)) # grab 20 random samples to plot
plotQualityProfile(fnFs[rand_samples])
}
# Reverse reads
# If the number of samples is 20 or less, plot them all, otherwise, just plot 20 randomly selected samples
if( length(fnRs) <= 20) {
plotQualityProfile(fnRs)
} else {
rand_samples <- sample(size = 20, 1:length(fnRs)) # grab 20 random samples to plot
plotQualityProfile(fnRs[rand_samples])
}
4 Filter parameter optimization with Figaro
Currently, Figaro (v1.1.1) only accepts files with Illumina naming convention, so we need to rename the files.
# get original file names
R1_names <- gsub(demultiplex_assigned_path , "", list.files(demultiplex_assigned_path , pattern="R1", full.names = TRUE))
# remove suffix
R1_names <- gsub("_R1.fastq.gz", "", R1_names)
# remove dots (Figaro v1.1.1 will throw an error if there dots in the sample name)
R1_names <- R1_names %>% str_replace_all("\\.", "")
# I'm not sure this is necessary, but anyway, I'm adding incrementing Sample digits after S in Illumina style
R1_names_incremented <- vector("character", length(R1_names))
for (i in seq_along(R1_names_incremented )) {
R1_names_incremented[[i]] <- paste0(R1_names[[i]], "_S", i)
}
# put names back together, appending Illumina naming convention, which is the format for later processing with Figaro
R1_names_incremented <- paste0(R1_names_incremented, "_L001_R1_001.fastq.gz")
# Now, rename files
file.rename(from = list.files(demultiplex_assigned_path , pattern="R1", full.names = TRUE), to = file.path(demultiplex_assigned_path, R1_names_incremented))## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
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## [121] TRUE TRUE TRUE TRUE TRUE TRUE TRUE# Repeat the above with the reverse reads
R2_names <- gsub(demultiplex_assigned_path , "", list.files(demultiplex_assigned_path , pattern="R2", full.names = TRUE))
R2_names <- gsub("_R2.fastq.gz", "", R2_names)
R2_names <- R2_names %>% str_replace_all("\\.", "")
R2_names_incremented <- vector("character", length(R2_names))
for (i in seq_along(R2_names_incremented )) {
R2_names_incremented[[i]] <- paste0(R2_names[[i]], "_S", i)
}
R2_names_incremented <- paste0(R2_names_incremented, "_L001_R2_001.fastq.gz")
file.rename(from = list.files(demultiplex_assigned_path , pattern="R2", full.names = TRUE), to = file.path(demultiplex_assigned_path, R2_names_incremented))## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
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## [121] TRUE TRUE TRUE TRUE TRUE TRUE TRUECheck that renaming worked
R1_names_incremented %>% head()## [1] "/04RNA1_S1_L001_R1_001.fastq.gz" "/04RNA2_S2_L001_R1_001.fastq.gz"
## [3] "/1041_S3_L001_R1_001.fastq.gz" "/1042_S4_L001_R1_001.fastq.gz"
## [5] "/1043_S5_L001_R1_001.fastq.gz" "/104RNA1_S6_L001_R1_001.fastq.gz"Create a directory for Figaro output
# Create directory to hold the output from figaro
if (!dir.exists(figaro_output_path)) dir.create(figaro_output_path)I couldn’t get figaro (v1.1.1) to run by system2() in R due to a shell permission denied error, but it worked on the command line. This chunk generates the exact text I entered in the command line after changing to the figaro directory. I then just read in the figaro output JSON and continue from there.
# text to change directory in terminal to figaro
paste("cd", figaro_path) %>% str_remove("/figaro.py") %>% cat()## cd /Users/melo.d/opt/figaro# The length of the amplified sequence target not including primers.
# Kraus et al. (in review) says the 515-Y M13 and 926R primer primer set produce gene fragments of ~400 bp
# primers total 60 bp
# sequences in 2X250 bp
# I originally tried 340 bp for figaro, but that resulted in low merged read percentage
# EK did not truncate left at all in her original processing
# Thus, I increased to 400
figaro_amplicon_length <- 400
figaro_min_overlap <- 20
figaro_output_file_name <- "Figaro_params_OM17.json"
flags_figaro <- paste("--ampliconLength", figaro_amplicon_length, "--forwardPrimerLength", FWD_length, "--reversePrimerLength", REV_length, "--outputFileName", figaro_output_file_name, "--inputDirectory", demultiplex_assigned_path, "--outputDirectory", figaro_output_path, "--minimumOverlap", figaro_min_overlap)
paste("python3", "figaro.py", flags_figaro) %>% cat()## python3 figaro.py --ampliconLength 400 --forwardPrimerLength 40 --reversePrimerLength 20 --outputFileName Figaro_params_OM17.json --inputDirectory /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/01_preprocess/demultiplexed/assigned --outputDirectory /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/01_preprocess/Figaro_output --minimumOverlap 20Read in Figaro JSON output, top 5 suggested trim parameters.
# Give the input file name to the function.
figaro_result <- fromJSON(file = file.path(figaro_output_path, figaro_output_file_name))
figaro_result[1:5] %>% paste(collapse = '\n') %>% cat()## list(trimPosition = c(236, 244), maxExpectedError = c(2, 4), readRetentionPercent = 87.41, score = 77.4082823910813)
## list(trimPosition = c(235, 245), maxExpectedError = c(2, 4), readRetentionPercent = 87.33, score = 77.3272346332589)
## list(trimPosition = c(234, 246), maxExpectedError = c(2, 4), readRetentionPercent = 87.28, score = 77.2832619135893)
## list(trimPosition = c(233, 247), maxExpectedError = c(2, 4), readRetentionPercent = 87.19, score = 77.1918676334917)
## list(trimPosition = c(232, 248), maxExpectedError = c(2, 4), readRetentionPercent = 87.12, score = 77.1177175571861)# Save and print Figaro-suggested parameters for dada2::filterAndTrim
(truncLen_best_figaro <- figaro_result[[1]]$trimPosition)## [1] 236 244(maxEE_best_figaro <- figaro_result[[1]]$maxExpectedError)## [1] 2 45 Filter and trim for quality
5.1 Organize file paths and directories
# set file path for quality-filtered read
filter_path <- file.path(project_path_OM17, "02_filter")
# Put filtered reads into separate sub-directories for big data workflow
if (!dir.exists(filter_path)) dir.create(filter_path)
subF_path <- file.path(filter_path, "preprocessed_F")
subR_path <- file.path(filter_path, "preprocessed_R")
if (!dir.exists(subF_path)) dir.create(subF_path)
if (!dir.exists(subR_path)) dir.create(subR_path)
# Move R1 and R2 from trimmed to separate forward/reverse sub-directories
# fnFs.Q <- file.path(subF_path, basename(fnFs))
# fnRs.Q <- file.path(subR_path, basename(fnRs))
fnFs.Q <- file.path(subF_path, basename(list.files(demultiplex_assigned_path , pattern="R1", full.names = TRUE)))
fnRs.Q <- file.path(subR_path, basename(list.files(demultiplex_assigned_path , pattern="R2", full.names = TRUE)))
file.rename(from = list.files(demultiplex_assigned_path , pattern="R1", full.names = TRUE), to = fnFs.Q)## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
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## [106] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [121] TRUE TRUE TRUE TRUE TRUE TRUE TRUEfile.rename(from = list.files(demultiplex_assigned_path , pattern="R2", full.names = TRUE), to = fnRs.Q)## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [76] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
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## [121] TRUE TRUE TRUE TRUE TRUE TRUE TRUE# File parsing; create file names and make sure that forward and reverse files match
filtpathF <- file.path(subF_path, "filtered") # files go into preprocessed_F/filtered/
filtpathR <- file.path(subR_path, "filtered") # ...
fastqFs <- sort(list.files(subF_path, pattern="fastq.gz"))
fastqRs <- sort(list.files(subR_path, pattern="fastq.gz"))
if(length(fastqFs) != length(fastqRs)) stop("Forward and reverse files do not match.")Before chosing sequence variants, we want to trim reads where their quality scores begin to drop (the truncLen and truncQ values) and remove any low-quality reads that are left over after we have finished trimming (the maxEE value).
5.2 Filter and trim
# also trimming lengths of primers in this step with trimLeft
filt_out <- filterAndTrim(fwd = file.path(subF_path, fastqFs), filt = file.path(filtpathF, fastqFs), rev = file.path(subR_path, fastqRs), filt.rev = file.path(filtpathR, fastqRs), trimLeft = c(FWD_length, REV_length), truncLen = truncLen_best_figaro, maxEE = maxEE_best_figaro, truncQ = 2, maxN = 0, rm.phix = TRUE, compress = TRUE, verbose = TRUE, multithread = TRUE)
# look at how many reads were kept
head(filt_out)## reads.in reads.out
## 04RNA1_S1_L001_R1_001.fastq.gz 7756 5911
## 04RNA2_S2_L001_R1_001.fastq.gz 4033 2848
## 1041_S3_L001_R1_001.fastq.gz 10611 9515
## 1042_S4_L001_R1_001.fastq.gz 17059 15301
## 1043_S5_L001_R1_001.fastq.gz 18852 16701
## 104RNA1_S6_L001_R1_001.fastq.gz 5320 4721# summary of samples in filt_out by percentage
filt_out %>%
data.frame() %>%
mutate(Samples = rownames(.),
percent_kept = 100*(reads.out/reads.in)) %>%
select(Samples, everything()) %>%
summarise(min_remaining = paste0(round(min(percent_kept), 2), "%"),
median_remaining = paste0(round(median(percent_kept), 2), "%"),
mean_remaining = paste0(round(mean(percent_kept), 2), "%"),
max_remaining = paste0(round(max(percent_kept), 2), "%"))5.3 Check if primers were removed by filterAndTrim
rbind(FWD.ForwardReads = sapply(FWD.orients, primerHits, fn=filtpathF[[1]]),
FWD.ReverseReads = sapply(FWD.orients, primerHits, fn=filtpathR[[1]]),
REV.ForwardReads = sapply(REV.orients, primerHits, fn=filtpathF[[1]]),
REV.ReverseReads = sapply(REV.orients, primerHits, fn=filtpathR[[1]]))## Forward Complement Reverse RevComp
## FWD.ForwardReads 1 0 0 1473
## FWD.ReverseReads 1 0 0 14134
## REV.ForwardReads 32 0 0 2622
## REV.ReverseReads 36 0 0 237The vast majority of primer hits were removed during filtering, but a considerable amount remain. These need to be removed. We will do so with cutadapt.
The primerHits function only scores a hit if the full primer sequence is found in the read. That would be 40 bases for the FWD primer or 20 for the REV primer in this case. The fact that so many full primer sequences remain in the reads after filtering suggest that they are internal (i.e. regular adapters as opposed to anchored adapters in the cutadapt lingo). So, let’s use regular adapters. However, to preserve the possibility that some biological reads happen by chance to be the same as the primer sequences, let’s increase the minimum overlap in cutadapt from the default of 3 bases to a somewhat more restrictive 5 bases for the REV primers and 7 bases for the FWD primer (because it is longer and thus more likely to have). Since reverse complements are found, let’s also enable reverse complements
6 Remove primers with cutadapt
6.1 Set up directories for cutadapt
# create directories to put the files trimmed by cutadapt
filt_and_cut_path_F <- file.path(subF_path, "filtered_and_cut")
filt_and_cut_path_R <- file.path(subR_path, "filtered_and_cut")
# Create directory to hold the output from cutadapt
if (!dir.exists(filt_and_cut_path_F)) dir.create(filt_and_cut_path_F)
if (!dir.exists(filt_and_cut_path_R)) dir.create(filt_and_cut_path_R)
filtfastqFs <- sort(file.path(filtpathF, list.files(filtpathF, pattern="fastq.gz")))
fnFs.cut <- file.path(filt_and_cut_path_F, basename(filtfastqFs))
filtfastqRs <- sort(file.path(filtpathR, list.files(filtpathR, pattern="fastq.gz")))
fnRs.cut <- file.path(filt_and_cut_path_R, basename(filtfastqRs))6.2 Run cutadapt
# Save the reverse complements of the primers to variables
FWD.RC <- dada2:::rc(FWD)
REV.RC <- dada2:::rc(REV)
# minimum length to output reads for cutadapt
minimum_length_cutadapt <- 50
# minimum overlap for "adapter" (barcode) to be detected by cutadapt
# minimum_overlap_cutadapt_FWD <- 5
# minimum_overlap_cutadapt_REV <- 7
minimum_overlap_cutadapt <- 5
## Create the cutadapt flags ##
# Trim FWD and the reverse-complement of REV off of R1 (forward reads)
R1.flags <- paste("-g", FWD, "-a", REV.RC)
# Trim REV and the reverse-complement of FWD off of R2 (reverse reads)
R2.flags <- paste("-G", REV, "-A", FWD.RC)
## Run Cutadapt
# default error rate of 10% applied
# https://cutadapt.readthedocs.io/en/stable/guide.html#error-tolerance
# I increased the minimum overlap from the default of 3 to 5 to reduce random matches
# https://cutadapt.readthedocs.io/en/stable/guide.html#minimum-overlap-reducing-random-matches
# -n 2 required to remove FWD and REV from reads
cutadapt_messages_2_list <- vector("list", length(filtfastqFs)) # set cutadapt message output list
for (i in seq_along(filtfastqFs)) {
cutadapt_messages_2_list[[i]] <- system2(cutadapt_path, args = c(R1.flags, R2.flags, "--overlap", minimum_overlap_cutadapt, "--minimum-length", minimum_length_cutadapt, "-n", 2, "-o", fnFs.cut[i], "-p", fnRs.cut[i], filtfastqFs[i], filtfastqRs[i]), stdout = TRUE, stderr = TRUE) # input files
}
cutadapt_messages_2_list # print output text## [[1]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/04RNA1_S1_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/04RNA1_S1_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/04RNA1_S1_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/04RNA1_S1_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.65 s (111 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 5,911"
## [9] " Read 1 with adapter: 29 (0.5%)"
## [10] " Read 2 with adapter: 626 (10.6%)"
## [11] "Pairs written (passing filters): 5,910 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 2,482,620 bp"
## [14] " Read 1: 1,158,556 bp"
## [15] " Read 2: 1,324,064 bp"
## [16] "Total written (filtered): 2,440,316 bp (98.3%)"
## [17] " Read 1: 1,157,062 bp"
## [18] " Read 2: 1,283,254 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 4 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "7\t1\t0.4\t0\t1"
## [30] "11\t1\t0.0\t1\t1"
## [31] "22\t1\t0.0\t2\t1"
## [32] "63\t1\t0.0\t4\t0 1"
## [33] ""
## [34] ""
## [35] "=== First read: Adapter 2 ==="
## [36] ""
## [37] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 25 times"
## [38] ""
## [39] "No. of allowed errors:"
## [40] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [41] ""
## [42] "Bases preceding removed adapters:"
## [43] " A: 4.0%"
## [44] " C: 4.0%"
## [45] " G: 84.0%"
## [46] " T: 8.0%"
## [47] " none/other: 0.0%"
## [48] "WARNING:"
## [49] " The adapter is preceded by \"G\" extremely often."
## [50] " The provided adapter sequence could be incomplete at its 3' end."
## [51] ""
## [52] "Overview of removed sequences"
## [53] "length\tcount\texpect\tmax.err\terror counts"
## [54] "7\t1\t0.4\t0\t1"
## [55] "8\t1\t0.1\t0\t1"
## [56] "18\t2\t0.0\t1\t2"
## [57] "36\t14\t0.0\t2\t14"
## [58] "62\t1\t0.0\t2\t1"
## [59] "74\t2\t0.0\t2\t2"
## [60] "82\t1\t0.0\t2\t1"
## [61] "90\t1\t0.0\t2\t1"
## [62] "118\t1\t0.0\t2\t1"
## [63] "140\t1\t0.0\t2\t1"
## [64] ""
## [65] ""
## [66] "=== Second read: Adapter 3 ==="
## [67] ""
## [68] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [69] ""
## [70] "=== Second read: Adapter 4 ==="
## [71] ""
## [72] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 626 times"
## [73] ""
## [74] "No. of allowed errors:"
## [75] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [76] ""
## [77] "Bases preceding removed adapters:"
## [78] " A: 95.5%"
## [79] " C: 3.4%"
## [80] " G: 0.2%"
## [81] " T: 1.0%"
## [82] " none/other: 0.0%"
## [83] "WARNING:"
## [84] " The adapter is preceded by \"A\" extremely often."
## [85] " The provided adapter sequence could be incomplete at its 3' end."
## [86] ""
## [87] "Overview of removed sequences"
## [88] "length\tcount\texpect\tmax.err\terror counts"
## [89] "5\t2\t5.8\t0\t2"
## [90] "6\t5\t1.4\t0\t5"
## [91] "7\t1\t0.4\t0\t1"
## [92] "8\t10\t0.1\t0\t10"
## [93] "10\t4\t0.0\t1\t3 1"
## [94] "12\t2\t0.0\t1\t2"
## [95] "13\t2\t0.0\t1\t2"
## [96] "14\t19\t0.0\t1\t17 2"
## [97] "15\t2\t0.0\t1\t2"
## [98] "16\t15\t0.0\t1\t14 1"
## [99] "17\t3\t0.0\t1\t3"
## [100] "18\t2\t0.0\t1\t2"
## [101] "19\t2\t0.0\t1\t2"
## [102] "20\t4\t0.0\t2\t3 1"
## [103] "21\t7\t0.0\t2\t7"
## [104] "22\t11\t0.0\t2\t11"
## [105] "23\t2\t0.0\t2\t2"
## [106] "25\t3\t0.0\t2\t3"
## [107] "26\t2\t0.0\t2\t0 2"
## [108] "27\t24\t0.0\t2\t17 6 1"
## [109] "28\t1\t0.0\t2\t1"
## [110] "29\t2\t0.0\t2\t1 1"
## [111] "30\t2\t0.0\t3\t2"
## [112] "31\t2\t0.0\t3\t1 0 1"
## [113] "32\t8\t0.0\t3\t7 1"
## [114] "33\t10\t0.0\t3\t8 1 0 1"
## [115] "34\t6\t0.0\t3\t5 1"
## [116] "35\t7\t0.0\t3\t6 1"
## [117] "36\t3\t0.0\t3\t2 0 1"
## [118] "38\t3\t0.0\t3\t2 1"
## [119] "39\t3\t0.0\t3\t3"
## [120] "40\t2\t0.0\t4\t1 1"
## [121] "41\t3\t0.0\t4\t2 1"
## [122] "42\t15\t0.0\t4\t12 1 0 2"
## [123] "43\t6\t0.0\t4\t5 1"
## [124] "44\t5\t0.0\t4\t3 2"
## [125] "45\t4\t0.0\t4\t2 1 1"
## [126] "46\t9\t0.0\t4\t8 0 0 1"
## [127] "47\t4\t0.0\t4\t3 0 1"
## [128] "48\t2\t0.0\t4\t2"
## [129] "50\t3\t0.0\t4\t3"
## [130] "51\t13\t0.0\t4\t10 1 1 1"
## [131] "52\t24\t0.0\t4\t21 1 1 0 1"
## [132] "53\t4\t0.0\t4\t4"
## [133] "54\t1\t0.0\t4\t1"
## [134] "55\t4\t0.0\t4\t4"
## [135] "56\t5\t0.0\t4\t4 1"
## [136] "57\t6\t0.0\t4\t3 3"
## [137] "58\t17\t0.0\t4\t15 1 1"
## [138] "59\t2\t0.0\t4\t1 1"
## [139] "60\t1\t0.0\t4\t1"
## [140] "61\t3\t0.0\t4\t3"
## [141] "62\t3\t0.0\t4\t3"
## [142] "63\t9\t0.0\t4\t9"
## [143] "64\t24\t0.0\t4\t23 1"
## [144] "65\t6\t0.0\t4\t6"
## [145] "66\t7\t0.0\t4\t6 1"
## [146] "67\t7\t0.0\t4\t5 2"
## [147] "68\t8\t0.0\t4\t7 1"
## [148] "69\t5\t0.0\t4\t5"
## [149] "70\t2\t0.0\t4\t2"
## [150] "71\t1\t0.0\t4\t1"
## [151] "72\t3\t0.0\t4\t3"
## [152] "73\t3\t0.0\t4\t3"
## [153] "74\t4\t0.0\t4\t3 0 0 0 1"
## [154] "75\t5\t0.0\t4\t5"
## [155] "76\t5\t0.0\t4\t5"
## [156] "77\t9\t0.0\t4\t9"
## [157] "78\t1\t0.0\t4\t1"
## [158] "79\t17\t0.0\t4\t14 2 1"
## [159] "80\t2\t0.0\t4\t2"
## [160] "81\t1\t0.0\t4\t1"
## [161] "83\t5\t0.0\t4\t3 1 0 1"
## [162] "84\t3\t0.0\t4\t3"
## [163] "85\t12\t0.0\t4\t11 1"
## [164] "86\t11\t0.0\t4\t9 2"
## [165] "87\t1\t0.0\t4\t1"
## [166] "88\t3\t0.0\t4\t3"
## [167] "89\t4\t0.0\t4\t3 1"
## [168] "90\t5\t0.0\t4\t5"
## [169] "91\t2\t0.0\t4\t2"
## [170] "92\t9\t0.0\t4\t9"
## [171] "93\t5\t0.0\t4\t4 1"
## [172] "94\t16\t0.0\t4\t12 3 1"
## [173] "95\t7\t0.0\t4\t7"
## [174] "96\t9\t0.0\t4\t8 1"
## [175] "98\t2\t0.0\t4\t2"
## [176] "99\t4\t0.0\t4\t4"
## [177] "100\t3\t0.0\t4\t3"
## [178] "101\t1\t0.0\t4\t1"
## [179] "102\t3\t0.0\t4\t3"
## [180] "103\t6\t0.0\t4\t5 0 1"
## [181] "104\t5\t0.0\t4\t4 1"
## [182] "105\t4\t0.0\t4\t4"
## [183] "106\t6\t0.0\t4\t5 1"
## [184] "107\t1\t0.0\t4\t1"
## [185] "108\t2\t0.0\t4\t2"
## [186] "109\t2\t0.0\t4\t1 1"
## [187] "110\t2\t0.0\t4\t1 1"
## [188] "111\t1\t0.0\t4\t1"
## [189] "112\t2\t0.0\t4\t2"
## [190] "113\t4\t0.0\t4\t4"
## [191] "114\t1\t0.0\t4\t1"
## [192] "115\t2\t0.0\t4\t2"
## [193] "116\t2\t0.0\t4\t2"
## [194] "117\t2\t0.0\t4\t1 1"
## [195] "118\t2\t0.0\t4\t2"
## [196] "119\t3\t0.0\t4\t2 1"
## [197] "121\t6\t0.0\t4\t6"
## [198] "124\t1\t0.0\t4\t1"
## [199] "125\t1\t0.0\t4\t1"
## [200] "126\t3\t0.0\t4\t3"
## [201] "128\t1\t0.0\t4\t1"
## [202] "129\t3\t0.0\t4\t2 1"
## [203] "132\t2\t0.0\t4\t2"
## [204] "133\t2\t0.0\t4\t2"
## [205] "136\t2\t0.0\t4\t1 0 1"
## [206] "137\t2\t0.0\t4\t2"
## [207] "140\t1\t0.0\t4\t0 1"
## [208] "142\t3\t0.0\t4\t3"
## [209] "143\t2\t0.0\t4\t2"
## [210] "144\t5\t0.0\t4\t5"
## [211] "145\t1\t0.0\t4\t1"
## [212] "146\t3\t0.0\t4\t3"
## [213] "147\t1\t0.0\t4\t0 1"
## [214] "148\t1\t0.0\t4\t1"
## [215] "151\t1\t0.0\t4\t1"
## [216] "152\t1\t0.0\t4\t1"
## [217] "155\t1\t0.0\t4\t1"
## [218] "159\t2\t0.0\t4\t2"
## [219] "162\t1\t0.0\t4\t1"
## [220] "165\t1\t0.0\t4\t1"
## [221] "168\t1\t0.0\t4\t1"
## [222] "173\t1\t0.0\t4\t1"
## [223] "175\t1\t0.0\t4\t1"
## [224] ""
## [225] ""
## [226] "WARNING:"
## [227] " One or more of your adapter sequences may be incomplete."
## [228] " Please see the detailed output above."
##
## [[2]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/04RNA2_S2_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/04RNA2_S2_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/04RNA2_S2_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/04RNA2_S2_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.32 s (114 us/read; 0.53 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 2,848"
## [9] " Read 1 with adapter: 10 (0.4%)"
## [10] " Read 2 with adapter: 209 (7.3%)"
## [11] "Pairs written (passing filters): 2,847 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 1,196,160 bp"
## [14] " Read 1: 558,208 bp"
## [15] " Read 2: 637,952 bp"
## [16] "Total written (filtered): 1,181,668 bp (98.8%)"
## [17] " Read 1: 557,498 bp"
## [18] " Read 2: 624,170 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "6\t1\t0.7\t0\t1"
## [30] "7\t1\t0.2\t0\t1"
## [31] "31\t1\t0.0\t3\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 7 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 28.6%"
## [43] " C: 0.0%"
## [44] " G: 71.4%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "36\t4\t0.0\t2\t4"
## [51] "90\t1\t0.0\t2\t1"
## [52] "118\t2\t0.0\t2\t2"
## [53] ""
## [54] ""
## [55] "=== Second read: Adapter 3 ==="
## [56] ""
## [57] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [58] ""
## [59] "=== Second read: Adapter 4 ==="
## [60] ""
## [61] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 209 times"
## [62] ""
## [63] "No. of allowed errors:"
## [64] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [65] ""
## [66] "Bases preceding removed adapters:"
## [67] " A: 93.8%"
## [68] " C: 5.3%"
## [69] " G: 0.5%"
## [70] " T: 0.5%"
## [71] " none/other: 0.0%"
## [72] "WARNING:"
## [73] " The adapter is preceded by \"A\" extremely often."
## [74] " The provided adapter sequence could be incomplete at its 3' end."
## [75] ""
## [76] "Overview of removed sequences"
## [77] "length\tcount\texpect\tmax.err\terror counts"
## [78] "5\t3\t2.8\t0\t3"
## [79] "6\t1\t0.7\t0\t1"
## [80] "8\t3\t0.0\t0\t3"
## [81] "9\t1\t0.0\t0\t1"
## [82] "10\t3\t0.0\t1\t2 1"
## [83] "11\t1\t0.0\t1\t1"
## [84] "12\t1\t0.0\t1\t1"
## [85] "14\t6\t0.0\t1\t4 2"
## [86] "15\t2\t0.0\t1\t2"
## [87] "16\t4\t0.0\t1\t4"
## [88] "17\t2\t0.0\t1\t2"
## [89] "18\t3\t0.0\t1\t3"
## [90] "21\t1\t0.0\t2\t1"
## [91] "22\t3\t0.0\t2\t2 1"
## [92] "23\t2\t0.0\t2\t2"
## [93] "24\t1\t0.0\t2\t1"
## [94] "26\t1\t0.0\t2\t1"
## [95] "27\t4\t0.0\t2\t3 1"
## [96] "29\t1\t0.0\t2\t1"
## [97] "30\t3\t0.0\t3\t2 1"
## [98] "33\t1\t0.0\t3\t1"
## [99] "34\t2\t0.0\t3\t1 0 1"
## [100] "35\t3\t0.0\t3\t3"
## [101] "36\t2\t0.0\t3\t2"
## [102] "38\t1\t0.0\t3\t1"
## [103] "40\t1\t0.0\t4\t1"
## [104] "41\t1\t0.0\t4\t1"
## [105] "42\t2\t0.0\t4\t2"
## [106] "43\t5\t0.0\t4\t5"
## [107] "44\t2\t0.0\t4\t2"
## [108] "45\t5\t0.0\t4\t3 2"
## [109] "46\t4\t0.0\t4\t3 0 1"
## [110] "47\t3\t0.0\t4\t3"
## [111] "50\t1\t0.0\t4\t0 0 0 0 1"
## [112] "51\t5\t0.0\t4\t4 1"
## [113] "52\t3\t0.0\t4\t3"
## [114] "53\t2\t0.0\t4\t2"
## [115] "54\t1\t0.0\t4\t1"
## [116] "55\t2\t0.0\t4\t1 0 1"
## [117] "57\t2\t0.0\t4\t1 1"
## [118] "58\t5\t0.0\t4\t5"
## [119] "59\t6\t0.0\t4\t5 1"
## [120] "60\t1\t0.0\t4\t0 1"
## [121] "62\t1\t0.0\t4\t1"
## [122] "63\t4\t0.0\t4\t4"
## [123] "64\t4\t0.0\t4\t4"
## [124] "65\t1\t0.0\t4\t1"
## [125] "67\t2\t0.0\t4\t2"
## [126] "68\t1\t0.0\t4\t1"
## [127] "69\t1\t0.0\t4\t0 1"
## [128] "70\t3\t0.0\t4\t3"
## [129] "72\t1\t0.0\t4\t1"
## [130] "73\t1\t0.0\t4\t1"
## [131] "74\t2\t0.0\t4\t2"
## [132] "75\t6\t0.0\t4\t6"
## [133] "76\t1\t0.0\t4\t1"
## [134] "77\t6\t0.0\t4\t6"
## [135] "79\t6\t0.0\t4\t4 1 1"
## [136] "84\t1\t0.0\t4\t1"
## [137] "85\t3\t0.0\t4\t3"
## [138] "86\t2\t0.0\t4\t2"
## [139] "87\t1\t0.0\t4\t1"
## [140] "90\t1\t0.0\t4\t1"
## [141] "92\t1\t0.0\t4\t1"
## [142] "93\t2\t0.0\t4\t2"
## [143] "94\t5\t0.0\t4\t4 1"
## [144] "96\t1\t0.0\t4\t1"
## [145] "99\t1\t0.0\t4\t1"
## [146] "102\t5\t0.0\t4\t4 1"
## [147] "103\t3\t0.0\t4\t3"
## [148] "104\t2\t0.0\t4\t2"
## [149] "105\t1\t0.0\t4\t1"
## [150] "108\t1\t0.0\t4\t1"
## [151] "111\t1\t0.0\t4\t1"
## [152] "113\t3\t0.0\t4\t3"
## [153] "114\t1\t0.0\t4\t0 0 0 1"
## [154] "115\t1\t0.0\t4\t1"
## [155] "116\t2\t0.0\t4\t2"
## [156] "117\t1\t0.0\t4\t0 1"
## [157] "118\t1\t0.0\t4\t1"
## [158] "120\t1\t0.0\t4\t1"
## [159] "121\t4\t0.0\t4\t4"
## [160] "123\t1\t0.0\t4\t1"
## [161] "127\t1\t0.0\t4\t1"
## [162] "128\t2\t0.0\t4\t2"
## [163] "132\t2\t0.0\t4\t2"
## [164] "134\t2\t0.0\t4\t2"
## [165] "138\t1\t0.0\t4\t1"
## [166] "142\t1\t0.0\t4\t1"
## [167] "146\t3\t0.0\t4\t3"
## [168] "154\t1\t0.0\t4\t1"
## [169] "157\t1\t0.0\t4\t1"
## [170] "163\t1\t0.0\t4\t1"
## [171] "170\t1\t0.0\t4\t1"
## [172] "183\t1\t0.0\t4\t1"
## [173] ""
## [174] ""
## [175] "WARNING:"
## [176] " One or more of your adapter sequences may be incomplete."
## [177] " Please see the detailed output above."
##
## [[3]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1041_S3_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1041_S3_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1041_S3_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1041_S3_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.13 s (118 us/read; 0.51 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 9,515"
## [9] " Read 1 with adapter: 21 (0.2%)"
## [10] " Read 2 with adapter: 136 (1.4%)"
## [11] "Pairs written (passing filters): 9,515 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,996,300 bp"
## [14] " Read 1: 1,864,940 bp"
## [15] " Read 2: 2,131,360 bp"
## [16] "Total written (filtered): 3,986,644 bp (99.8%)"
## [17] " Read 1: 1,863,964 bp"
## [18] " Read 2: 2,122,680 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 6 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t9.3\t0\t1"
## [30] "7\t2\t0.6\t0\t2"
## [31] "18\t1\t0.0\t1\t0 1"
## [32] "23\t2\t0.0\t2\t2"
## [33] ""
## [34] ""
## [35] "=== First read: Adapter 2 ==="
## [36] ""
## [37] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 15 times"
## [38] ""
## [39] "No. of allowed errors:"
## [40] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [41] ""
## [42] "Bases preceding removed adapters:"
## [43] " A: 0.0%"
## [44] " C: 33.3%"
## [45] " G: 66.7%"
## [46] " T: 0.0%"
## [47] " none/other: 0.0%"
## [48] ""
## [49] "Overview of removed sequences"
## [50] "length\tcount\texpect\tmax.err\terror counts"
## [51] "27\t4\t0.0\t2\t4"
## [52] "66\t10\t0.0\t2\t9 1"
## [53] "125\t1\t0.0\t2\t1"
## [54] ""
## [55] ""
## [56] "=== Second read: Adapter 3 ==="
## [57] ""
## [58] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [59] ""
## [60] "=== Second read: Adapter 4 ==="
## [61] ""
## [62] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 136 times"
## [63] ""
## [64] "No. of allowed errors:"
## [65] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [66] ""
## [67] "Bases preceding removed adapters:"
## [68] " A: 66.9%"
## [69] " C: 22.1%"
## [70] " G: 7.4%"
## [71] " T: 3.7%"
## [72] " none/other: 0.0%"
## [73] ""
## [74] "Overview of removed sequences"
## [75] "length\tcount\texpect\tmax.err\terror counts"
## [76] "5\t9\t9.3\t0\t9"
## [77] "6\t1\t2.3\t0\t1"
## [78] "7\t3\t0.6\t0\t3"
## [79] "8\t1\t0.1\t0\t1"
## [80] "14\t2\t0.0\t1\t1 1"
## [81] "15\t1\t0.0\t1\t1"
## [82] "16\t1\t0.0\t1\t1"
## [83] "17\t2\t0.0\t1\t2"
## [84] "18\t1\t0.0\t1\t1"
## [85] "19\t2\t0.0\t1\t2"
## [86] "20\t3\t0.0\t2\t3"
## [87] "21\t1\t0.0\t2\t1"
## [88] "22\t1\t0.0\t2\t1"
## [89] "23\t3\t0.0\t2\t1 2"
## [90] "27\t2\t0.0\t2\t2"
## [91] "28\t2\t0.0\t2\t2"
## [92] "30\t2\t0.0\t3\t1 1"
## [93] "31\t1\t0.0\t3\t0 1"
## [94] "32\t2\t0.0\t3\t2"
## [95] "33\t2\t0.0\t3\t1 1"
## [96] "35\t1\t0.0\t3\t0 1"
## [97] "37\t3\t0.0\t3\t2 1"
## [98] "38\t2\t0.0\t3\t1 0 0 1"
## [99] "40\t1\t0.0\t4\t1"
## [100] "41\t3\t0.0\t4\t2 1"
## [101] "42\t1\t0.0\t4\t1"
## [102] "43\t1\t0.0\t4\t0 0 1"
## [103] "46\t1\t0.0\t4\t1"
## [104] "47\t3\t0.0\t4\t2 0 1"
## [105] "51\t1\t0.0\t4\t1"
## [106] "52\t2\t0.0\t4\t1 0 1"
## [107] "55\t4\t0.0\t4\t4"
## [108] "56\t1\t0.0\t4\t1"
## [109] "57\t1\t0.0\t4\t1"
## [110] "58\t1\t0.0\t4\t1"
## [111] "59\t1\t0.0\t4\t1"
## [112] "60\t3\t0.0\t4\t2 1"
## [113] "63\t1\t0.0\t4\t1"
## [114] "66\t2\t0.0\t4\t1 0 1"
## [115] "67\t1\t0.0\t4\t1"
## [116] "68\t1\t0.0\t4\t1"
## [117] "71\t1\t0.0\t4\t1"
## [118] "72\t1\t0.0\t4\t1"
## [119] "73\t1\t0.0\t4\t1"
## [120] "74\t1\t0.0\t4\t1"
## [121] "75\t2\t0.0\t4\t2"
## [122] "77\t1\t0.0\t4\t1"
## [123] "79\t1\t0.0\t4\t1"
## [124] "83\t1\t0.0\t4\t1"
## [125] "84\t1\t0.0\t4\t1"
## [126] "86\t2\t0.0\t4\t2"
## [127] "87\t3\t0.0\t4\t1 2"
## [128] "89\t1\t0.0\t4\t1"
## [129] "90\t3\t0.0\t4\t3"
## [130] "93\t1\t0.0\t4\t1"
## [131] "94\t12\t0.0\t4\t10 2"
## [132] "95\t2\t0.0\t4\t2"
## [133] "97\t1\t0.0\t4\t1"
## [134] "98\t1\t0.0\t4\t1"
## [135] "99\t1\t0.0\t4\t1"
## [136] "105\t1\t0.0\t4\t1"
## [137] "107\t1\t0.0\t4\t1"
## [138] "108\t1\t0.0\t4\t1"
## [139] "109\t1\t0.0\t4\t1"
## [140] "113\t1\t0.0\t4\t1"
## [141] "114\t1\t0.0\t4\t1"
## [142] "118\t1\t0.0\t4\t1"
## [143] "121\t1\t0.0\t4\t1"
## [144] "128\t1\t0.0\t4\t1"
## [145] "130\t1\t0.0\t4\t1"
## [146] "131\t1\t0.0\t4\t1"
## [147] "133\t1\t0.0\t4\t1"
## [148] "134\t2\t0.0\t4\t2"
## [149] "142\t1\t0.0\t4\t1"
## [150] "147\t1\t0.0\t4\t1"
## [151] "150\t1\t0.0\t4\t1"
## [152] "153\t2\t0.0\t4\t2"
## [153] "157\t1\t0.0\t4\t1"
## [154] "163\t1\t0.0\t4\t1"
## [155] "166\t1\t0.0\t4\t0 0 1"
##
## [[4]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1042_S4_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1042_S4_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1042_S4_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1042_S4_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.82 s (119 us/read; 0.50 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 15,301"
## [9] " Read 1 with adapter: 26 (0.2%)"
## [10] " Read 2 with adapter: 166 (1.1%)"
## [11] "Pairs written (passing filters): 15,301 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 6,426,420 bp"
## [14] " Read 1: 2,998,996 bp"
## [15] " Read 2: 3,427,424 bp"
## [16] "Total written (filtered): 6,414,209 bp (99.8%)"
## [17] " Read 1: 2,997,392 bp"
## [18] " Read 2: 3,416,817 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 1 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "13\t1\t0.0\t1\t1"
## [30] ""
## [31] ""
## [32] "=== First read: Adapter 2 ==="
## [33] ""
## [34] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 25 times"
## [35] ""
## [36] "No. of allowed errors:"
## [37] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [38] ""
## [39] "Bases preceding removed adapters:"
## [40] " A: 4.0%"
## [41] " C: 0.0%"
## [42] " G: 96.0%"
## [43] " T: 0.0%"
## [44] " none/other: 0.0%"
## [45] "WARNING:"
## [46] " The adapter is preceded by \"G\" extremely often."
## [47] " The provided adapter sequence could be incomplete at its 3' end."
## [48] ""
## [49] "Overview of removed sequences"
## [50] "length\tcount\texpect\tmax.err\terror counts"
## [51] "6\t1\t3.7\t0\t1"
## [52] "66\t23\t0.0\t2\t23"
## [53] "67\t1\t0.0\t2\t1"
## [54] ""
## [55] ""
## [56] "=== Second read: Adapter 3 ==="
## [57] ""
## [58] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [59] ""
## [60] "=== Second read: Adapter 4 ==="
## [61] ""
## [62] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 166 times"
## [63] ""
## [64] "No. of allowed errors:"
## [65] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [66] ""
## [67] "Bases preceding removed adapters:"
## [68] " A: 66.9%"
## [69] " C: 26.5%"
## [70] " G: 3.6%"
## [71] " T: 3.0%"
## [72] " none/other: 0.0%"
## [73] ""
## [74] "Overview of removed sequences"
## [75] "length\tcount\texpect\tmax.err\terror counts"
## [76] "5\t13\t14.9\t0\t13"
## [77] "6\t2\t3.7\t0\t2"
## [78] "7\t1\t0.9\t0\t1"
## [79] "8\t8\t0.2\t0\t8"
## [80] "10\t1\t0.0\t1\t1"
## [81] "11\t1\t0.0\t1\t1"
## [82] "12\t1\t0.0\t1\t1"
## [83] "15\t3\t0.0\t1\t3"
## [84] "16\t3\t0.0\t1\t3"
## [85] "20\t4\t0.0\t2\t3 0 1"
## [86] "21\t2\t0.0\t2\t1 1"
## [87] "22\t2\t0.0\t2\t0 2"
## [88] "23\t1\t0.0\t2\t1"
## [89] "24\t1\t0.0\t2\t1"
## [90] "25\t1\t0.0\t2\t1"
## [91] "27\t1\t0.0\t2\t1"
## [92] "28\t1\t0.0\t2\t1"
## [93] "29\t1\t0.0\t2\t1"
## [94] "33\t2\t0.0\t3\t1 1"
## [95] "35\t1\t0.0\t3\t1"
## [96] "36\t5\t0.0\t3\t4 1"
## [97] "38\t1\t0.0\t3\t1"
## [98] "40\t3\t0.0\t4\t3"
## [99] "41\t1\t0.0\t4\t1"
## [100] "42\t3\t0.0\t4\t0 0 3"
## [101] "43\t1\t0.0\t4\t1"
## [102] "46\t2\t0.0\t4\t2"
## [103] "47\t2\t0.0\t4\t1 1"
## [104] "50\t2\t0.0\t4\t2"
## [105] "51\t3\t0.0\t4\t3"
## [106] "52\t4\t0.0\t4\t4"
## [107] "55\t1\t0.0\t4\t1"
## [108] "61\t1\t0.0\t4\t1"
## [109] "62\t1\t0.0\t4\t0 1"
## [110] "63\t2\t0.0\t4\t2"
## [111] "70\t1\t0.0\t4\t0 1"
## [112] "72\t2\t0.0\t4\t2"
## [113] "73\t3\t0.0\t4\t3"
## [114] "74\t1\t0.0\t4\t1"
## [115] "76\t2\t0.0\t4\t2"
## [116] "81\t1\t0.0\t4\t1"
## [117] "82\t1\t0.0\t4\t1"
## [118] "83\t1\t0.0\t4\t0 1"
## [119] "84\t1\t0.0\t4\t1"
## [120] "85\t2\t0.0\t4\t2"
## [121] "86\t1\t0.0\t4\t1"
## [122] "87\t2\t0.0\t4\t2"
## [123] "88\t1\t0.0\t4\t1"
## [124] "89\t3\t0.0\t4\t3"
## [125] "90\t1\t0.0\t4\t1"
## [126] "92\t1\t0.0\t4\t1"
## [127] "93\t1\t0.0\t4\t1"
## [128] "94\t25\t0.0\t4\t20 5"
## [129] "98\t4\t0.0\t4\t3 1"
## [130] "99\t1\t0.0\t4\t1"
## [131] "100\t2\t0.0\t4\t2"
## [132] "103\t1\t0.0\t4\t1"
## [133] "104\t1\t0.0\t4\t1"
## [134] "105\t7\t0.0\t4\t6 1"
## [135] "108\t1\t0.0\t4\t1"
## [136] "109\t1\t0.0\t4\t1"
## [137] "113\t1\t0.0\t4\t1"
## [138] "114\t1\t0.0\t4\t1"
## [139] "115\t1\t0.0\t4\t1"
## [140] "116\t1\t0.0\t4\t1"
## [141] "125\t2\t0.0\t4\t2"
## [142] "133\t1\t0.0\t4\t1"
## [143] "134\t2\t0.0\t4\t2"
## [144] "135\t1\t0.0\t4\t1"
## [145] "139\t1\t0.0\t4\t1"
## [146] "143\t1\t0.0\t4\t1"
## [147] "147\t1\t0.0\t4\t1"
## [148] "148\t1\t0.0\t4\t1"
## [149] "170\t1\t0.0\t4\t1"
## [150] "171\t1\t0.0\t4\t1"
## [151] ""
## [152] ""
## [153] "WARNING:"
## [154] " One or more of your adapter sequences may be incomplete."
## [155] " Please see the detailed output above."
##
## [[5]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1043_S5_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1043_S5_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1043_S5_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1043_S5_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.98 s (119 us/read; 0.51 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 16,701"
## [9] " Read 1 with adapter: 22 (0.1%)"
## [10] " Read 2 with adapter: 153 (0.9%)"
## [11] "Pairs written (passing filters): 16,700 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 7,014,420 bp"
## [14] " Read 1: 3,273,396 bp"
## [15] " Read 2: 3,741,024 bp"
## [16] "Total written (filtered): 7,004,720 bp (99.9%)"
## [17] " Read 1: 3,272,220 bp"
## [18] " Read 2: 3,732,500 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 2 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "11\t2\t0.0\t1\t2"
## [30] ""
## [31] ""
## [32] "=== First read: Adapter 2 ==="
## [33] ""
## [34] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 20 times"
## [35] ""
## [36] "No. of allowed errors:"
## [37] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [38] ""
## [39] "Bases preceding removed adapters:"
## [40] " A: 30.0%"
## [41] " C: 0.0%"
## [42] " G: 70.0%"
## [43] " T: 0.0%"
## [44] " none/other: 0.0%"
## [45] ""
## [46] "Overview of removed sequences"
## [47] "length\tcount\texpect\tmax.err\terror counts"
## [48] "12\t5\t0.0\t1\t5"
## [49] "13\t1\t0.0\t1\t1"
## [50] "26\t1\t0.0\t2\t1"
## [51] "66\t12\t0.0\t2\t12"
## [52] "67\t1\t0.0\t2\t1"
## [53] ""
## [54] ""
## [55] "=== Second read: Adapter 3 ==="
## [56] ""
## [57] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [58] ""
## [59] "No. of allowed errors:"
## [60] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [61] ""
## [62] "Overview of removed sequences"
## [63] "length\tcount\texpect\tmax.err\terror counts"
## [64] "7\t1\t1.0\t0\t1"
## [65] ""
## [66] ""
## [67] "=== Second read: Adapter 4 ==="
## [68] ""
## [69] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 152 times"
## [70] ""
## [71] "No. of allowed errors:"
## [72] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [73] ""
## [74] "Bases preceding removed adapters:"
## [75] " A: 63.2%"
## [76] " C: 23.7%"
## [77] " G: 3.3%"
## [78] " T: 9.9%"
## [79] " none/other: 0.0%"
## [80] ""
## [81] "Overview of removed sequences"
## [82] "length\tcount\texpect\tmax.err\terror counts"
## [83] "5\t15\t16.3\t0\t15"
## [84] "6\t1\t4.1\t0\t1"
## [85] "7\t2\t1.0\t0\t2"
## [86] "8\t8\t0.3\t0\t8"
## [87] "9\t1\t0.1\t0\t1"
## [88] "10\t3\t0.0\t1\t1 2"
## [89] "12\t1\t0.0\t1\t1"
## [90] "14\t1\t0.0\t1\t1"
## [91] "15\t2\t0.0\t1\t2"
## [92] "16\t1\t0.0\t1\t1"
## [93] "17\t1\t0.0\t1\t1"
## [94] "18\t1\t0.0\t1\t1"
## [95] "20\t1\t0.0\t2\t1"
## [96] "21\t1\t0.0\t2\t1"
## [97] "22\t4\t0.0\t2\t3 1"
## [98] "23\t4\t0.0\t2\t3 1"
## [99] "24\t2\t0.0\t2\t0 2"
## [100] "27\t1\t0.0\t2\t1"
## [101] "31\t1\t0.0\t3\t1"
## [102] "32\t1\t0.0\t3\t0 0 0 1"
## [103] "34\t3\t0.0\t3\t3"
## [104] "35\t6\t0.0\t3\t6"
## [105] "36\t1\t0.0\t3\t1"
## [106] "39\t1\t0.0\t3\t1"
## [107] "40\t5\t0.0\t4\t3 1 1"
## [108] "41\t1\t0.0\t4\t0 1"
## [109] "42\t1\t0.0\t4\t1"
## [110] "46\t2\t0.0\t4\t1 1"
## [111] "47\t2\t0.0\t4\t2"
## [112] "48\t1\t0.0\t4\t0 1"
## [113] "52\t2\t0.0\t4\t2"
## [114] "54\t2\t0.0\t4\t2"
## [115] "55\t2\t0.0\t4\t1 0 0 0 1"
## [116] "58\t1\t0.0\t4\t1"
## [117] "59\t1\t0.0\t4\t1"
## [118] "60\t1\t0.0\t4\t1"
## [119] "61\t3\t0.0\t4\t3"
## [120] "63\t1\t0.0\t4\t1"
## [121] "65\t1\t0.0\t4\t0 1"
## [122] "66\t1\t0.0\t4\t1"
## [123] "67\t1\t0.0\t4\t1"
## [124] "70\t1\t0.0\t4\t0 1"
## [125] "72\t1\t0.0\t4\t0 1"
## [126] "73\t2\t0.0\t4\t1 1"
## [127] "74\t1\t0.0\t4\t1"
## [128] "75\t2\t0.0\t4\t2"
## [129] "79\t2\t0.0\t4\t2"
## [130] "80\t2\t0.0\t4\t2"
## [131] "82\t3\t0.0\t4\t3"
## [132] "83\t1\t0.0\t4\t0 1"
## [133] "84\t3\t0.0\t4\t2 1"
## [134] "85\t2\t0.0\t4\t2"
## [135] "86\t2\t0.0\t4\t2"
## [136] "87\t1\t0.0\t4\t1"
## [137] "91\t1\t0.0\t4\t1"
## [138] "93\t1\t0.0\t4\t1"
## [139] "94\t13\t0.0\t4\t10 2 1"
## [140] "98\t1\t0.0\t4\t1"
## [141] "99\t5\t0.0\t4\t5"
## [142] "102\t1\t0.0\t4\t0 0 1"
## [143] "105\t3\t0.0\t4\t2 1"
## [144] "107\t1\t0.0\t4\t0 1"
## [145] "113\t1\t0.0\t4\t1"
## [146] "117\t1\t0.0\t4\t1"
## [147] "119\t1\t0.0\t4\t1"
## [148] "121\t1\t0.0\t4\t1"
## [149] "127\t2\t0.0\t4\t2"
## [150] "128\t1\t0.0\t4\t1"
## [151] "132\t1\t0.0\t4\t1"
## [152] "135\t1\t0.0\t4\t1"
## [153] "146\t1\t0.0\t4\t1"
## [154] "154\t1\t0.0\t4\t1"
## [155] "177\t1\t0.0\t4\t1"
##
## [[6]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/104RNA1_S6_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/104RNA1_S6_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/104RNA1_S6_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/104RNA1_S6_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.55 s (117 us/read; 0.51 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 4,721"
## [9] " Read 1 with adapter: 8 (0.2%)"
## [10] " Read 2 with adapter: 349 (7.4%)"
## [11] "Pairs written (passing filters): 4,719 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 1,982,820 bp"
## [14] " Read 1: 925,316 bp"
## [15] " Read 2: 1,057,504 bp"
## [16] "Total written (filtered): 1,957,358 bp (98.7%)"
## [17] " Read 1: 924,331 bp"
## [18] " Read 2: 1,033,027 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 8 times"
## [27] ""
## [28] "No. of allowed errors:"
## [29] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [30] ""
## [31] "Bases preceding removed adapters:"
## [32] " A: 12.5%"
## [33] " C: 12.5%"
## [34] " G: 75.0%"
## [35] " T: 0.0%"
## [36] " none/other: 0.0%"
## [37] ""
## [38] "Overview of removed sequences"
## [39] "length\tcount\texpect\tmax.err\terror counts"
## [40] "6\t1\t1.2\t0\t1"
## [41] "10\t1\t0.0\t1\t1"
## [42] "82\t2\t0.0\t2\t2"
## [43] "88\t1\t0.0\t2\t1"
## [44] "90\t1\t0.0\t2\t1"
## [45] "92\t1\t0.0\t2\t1"
## [46] "143\t1\t0.0\t2\t1"
## [47] ""
## [48] ""
## [49] "=== Second read: Adapter 3 ==="
## [50] ""
## [51] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 6 times"
## [52] ""
## [53] "No. of allowed errors:"
## [54] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [55] ""
## [56] "Overview of removed sequences"
## [57] "length\tcount\texpect\tmax.err\terror counts"
## [58] "5\t1\t4.6\t0\t1"
## [59] "12\t5\t0.0\t1\t5"
## [60] ""
## [61] ""
## [62] "=== Second read: Adapter 4 ==="
## [63] ""
## [64] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 344 times"
## [65] ""
## [66] "No. of allowed errors:"
## [67] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [68] ""
## [69] "Bases preceding removed adapters:"
## [70] " A: 83.1%"
## [71] " C: 13.4%"
## [72] " G: 0.6%"
## [73] " T: 2.9%"
## [74] " none/other: 0.0%"
## [75] "WARNING:"
## [76] " The adapter is preceded by \"A\" extremely often."
## [77] " The provided adapter sequence could be incomplete at its 3' end."
## [78] ""
## [79] "Overview of removed sequences"
## [80] "length\tcount\texpect\tmax.err\terror counts"
## [81] "5\t1\t4.6\t0\t1"
## [82] "6\t2\t1.2\t0\t2"
## [83] "7\t2\t0.3\t0\t2"
## [84] "8\t4\t0.1\t0\t4"
## [85] "10\t2\t0.0\t1\t2"
## [86] "11\t1\t0.0\t1\t1"
## [87] "12\t3\t0.0\t1\t3"
## [88] "13\t2\t0.0\t1\t2"
## [89] "14\t3\t0.0\t1\t3"
## [90] "15\t4\t0.0\t1\t4"
## [91] "16\t1\t0.0\t1\t1"
## [92] "17\t2\t0.0\t1\t2"
## [93] "18\t1\t0.0\t1\t0 1"
## [94] "19\t1\t0.0\t1\t1"
## [95] "20\t3\t0.0\t2\t3"
## [96] "21\t5\t0.0\t2\t5"
## [97] "22\t3\t0.0\t2\t3"
## [98] "23\t3\t0.0\t2\t2 1"
## [99] "24\t2\t0.0\t2\t2"
## [100] "25\t4\t0.0\t2\t3 0 1"
## [101] "26\t1\t0.0\t2\t1"
## [102] "27\t4\t0.0\t2\t3 1"
## [103] "29\t2\t0.0\t2\t1 0 1"
## [104] "30\t2\t0.0\t3\t1 0 0 1"
## [105] "32\t4\t0.0\t3\t3 1"
## [106] "33\t4\t0.0\t3\t1 3"
## [107] "34\t4\t0.0\t3\t3 1"
## [108] "35\t3\t0.0\t3\t2 0 1"
## [109] "37\t1\t0.0\t3\t1"
## [110] "38\t3\t0.0\t3\t2 1"
## [111] "39\t1\t0.0\t3\t0 0 1"
## [112] "40\t3\t0.0\t4\t1 2"
## [113] "41\t2\t0.0\t4\t1 1"
## [114] "42\t7\t0.0\t4\t6 1"
## [115] "43\t1\t0.0\t4\t1"
## [116] "44\t2\t0.0\t4\t2"
## [117] "45\t5\t0.0\t4\t3 2"
## [118] "46\t6\t0.0\t4\t3 2 0 1"
## [119] "47\t5\t0.0\t4\t3 2"
## [120] "49\t1\t0.0\t4\t0 1"
## [121] "50\t2\t0.0\t4\t2"
## [122] "51\t8\t0.0\t4\t7 0 1"
## [123] "52\t11\t0.0\t4\t9 1 0 1"
## [124] "53\t1\t0.0\t4\t1"
## [125] "54\t2\t0.0\t4\t1 1"
## [126] "55\t3\t0.0\t4\t2 0 0 1"
## [127] "56\t3\t0.0\t4\t3"
## [128] "57\t7\t0.0\t4\t3 4"
## [129] "58\t3\t0.0\t4\t3"
## [130] "59\t3\t0.0\t4\t3"
## [131] "60\t3\t0.0\t4\t3"
## [132] "61\t1\t0.0\t4\t0 1"
## [133] "63\t2\t0.0\t4\t1 1"
## [134] "64\t7\t0.0\t4\t7"
## [135] "65\t6\t0.0\t4\t6"
## [136] "66\t3\t0.0\t4\t3"
## [137] "67\t1\t0.0\t4\t1"
## [138] "69\t2\t0.0\t4\t2"
## [139] "70\t1\t0.0\t4\t1"
## [140] "72\t4\t0.0\t4\t3 1"
## [141] "73\t4\t0.0\t4\t4"
## [142] "74\t2\t0.0\t4\t2"
## [143] "75\t4\t0.0\t4\t4"
## [144] "76\t8\t0.0\t4\t8"
## [145] "78\t2\t0.0\t4\t2"
## [146] "79\t7\t0.0\t4\t6 1"
## [147] "81\t2\t0.0\t4\t1 1"
## [148] "82\t1\t0.0\t4\t1"
## [149] "83\t4\t0.0\t4\t4"
## [150] "84\t3\t0.0\t4\t3"
## [151] "85\t2\t0.0\t4\t2"
## [152] "86\t13\t0.0\t4\t11 2"
## [153] "87\t2\t0.0\t4\t2"
## [154] "88\t3\t0.0\t4\t3"
## [155] "89\t3\t0.0\t4\t2 1"
## [156] "91\t1\t0.0\t4\t1"
## [157] "92\t3\t0.0\t4\t2 0 1"
## [158] "93\t4\t0.0\t4\t4"
## [159] "94\t6\t0.0\t4\t6"
## [160] "95\t3\t0.0\t4\t3"
## [161] "96\t5\t0.0\t4\t5"
## [162] "97\t1\t0.0\t4\t1"
## [163] "99\t1\t0.0\t4\t1"
## [164] "100\t1\t0.0\t4\t1"
## [165] "101\t2\t0.0\t4\t2"
## [166] "102\t2\t0.0\t4\t2"
## [167] "103\t1\t0.0\t4\t1"
## [168] "104\t1\t0.0\t4\t0 1"
## [169] "105\t1\t0.0\t4\t1"
## [170] "106\t2\t0.0\t4\t2"
## [171] "107\t1\t0.0\t4\t1"
## [172] "110\t3\t0.0\t4\t3"
## [173] "111\t3\t0.0\t4\t3"
## [174] "112\t2\t0.0\t4\t1 1"
## [175] "113\t2\t0.0\t4\t2"
## [176] "115\t5\t0.0\t4\t5"
## [177] "116\t3\t0.0\t4\t2 1"
## [178] "117\t1\t0.0\t4\t1"
## [179] "118\t3\t0.0\t4\t2 1"
## [180] "119\t1\t0.0\t4\t1"
## [181] "120\t1\t0.0\t4\t1"
## [182] "121\t2\t0.0\t4\t2"
## [183] "122\t2\t0.0\t4\t2"
## [184] "123\t2\t0.0\t4\t2"
## [185] "125\t1\t0.0\t4\t1"
## [186] "126\t2\t0.0\t4\t2"
## [187] "127\t2\t0.0\t4\t2"
## [188] "128\t2\t0.0\t4\t2"
## [189] "129\t1\t0.0\t4\t1"
## [190] "130\t2\t0.0\t4\t2"
## [191] "131\t1\t0.0\t4\t1"
## [192] "133\t3\t0.0\t4\t3"
## [193] "134\t1\t0.0\t4\t1"
## [194] "135\t2\t0.0\t4\t2"
## [195] "137\t1\t0.0\t4\t1"
## [196] "139\t1\t0.0\t4\t1"
## [197] "140\t1\t0.0\t4\t1"
## [198] "141\t2\t0.0\t4\t1 1"
## [199] "142\t1\t0.0\t4\t1"
## [200] "144\t1\t0.0\t4\t1"
## [201] "146\t1\t0.0\t4\t1"
## [202] "147\t1\t0.0\t4\t1"
## [203] "148\t1\t0.0\t4\t1"
## [204] "150\t1\t0.0\t4\t1"
## [205] "156\t2\t0.0\t4\t2"
## [206] "162\t1\t0.0\t4\t1"
## [207] "166\t1\t0.0\t4\t1"
## [208] "171\t1\t0.0\t4\t1"
## [209] "173\t1\t0.0\t4\t1"
## [210] "175\t1\t0.0\t4\t1"
## [211] "180\t1\t0.0\t4\t1"
## [212] ""
## [213] ""
## [214] "WARNING:"
## [215] " One or more of your adapter sequences may be incomplete."
## [216] " Please see the detailed output above."
##
## [[7]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/104RNA2_S7_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/104RNA2_S7_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/104RNA2_S7_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/104RNA2_S7_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.50 s (121 us/read; 0.49 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 12,360"
## [9] " Read 1 with adapter: 43 (0.3%)"
## [10] " Read 2 with adapter: 547 (4.4%)"
## [11] "Pairs written (passing filters): 12,359 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 5,191,200 bp"
## [14] " Read 1: 2,422,560 bp"
## [15] " Read 2: 2,768,640 bp"
## [16] "Total written (filtered): 5,150,661 bp (99.2%)"
## [17] " Read 1: 2,419,806 bp"
## [18] " Read 2: 2,730,855 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 5 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "15\t1\t0.0\t1\t1"
## [30] "18\t1\t0.0\t1\t1"
## [31] "20\t1\t0.0\t2\t1"
## [32] "31\t1\t0.0\t3\t1"
## [33] "33\t1\t0.0\t3\t0 1"
## [34] ""
## [35] ""
## [36] "=== First read: Adapter 2 ==="
## [37] ""
## [38] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 38 times"
## [39] ""
## [40] "No. of allowed errors:"
## [41] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [42] ""
## [43] "Bases preceding removed adapters:"
## [44] " A: 18.4%"
## [45] " C: 7.9%"
## [46] " G: 73.7%"
## [47] " T: 0.0%"
## [48] " none/other: 0.0%"
## [49] ""
## [50] "Overview of removed sequences"
## [51] "length\tcount\texpect\tmax.err\terror counts"
## [52] "7\t1\t0.8\t0\t1"
## [53] "10\t1\t0.0\t1\t0 1"
## [54] "11\t1\t0.0\t1\t1"
## [55] "13\t1\t0.0\t1\t1"
## [56] "14\t1\t0.0\t1\t1"
## [57] "17\t1\t0.0\t1\t1"
## [58] "36\t5\t0.0\t2\t5"
## [59] "44\t1\t0.0\t2\t1"
## [60] "45\t3\t0.0\t2\t3"
## [61] "56\t1\t0.0\t2\t1"
## [62] "59\t1\t0.0\t2\t1"
## [63] "72\t1\t0.0\t2\t1"
## [64] "82\t4\t0.0\t2\t4"
## [65] "90\t8\t0.0\t2\t8"
## [66] "91\t1\t0.0\t2\t1"
## [67] "99\t1\t0.0\t2\t1"
## [68] "116\t1\t0.0\t2\t1"
## [69] "117\t3\t0.0\t2\t3"
## [70] "118\t1\t0.0\t2\t1"
## [71] "157\t1\t0.0\t2\t1"
## [72] ""
## [73] ""
## [74] "=== Second read: Adapter 3 ==="
## [75] ""
## [76] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 2 times"
## [77] ""
## [78] "No. of allowed errors:"
## [79] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [80] ""
## [81] "Overview of removed sequences"
## [82] "length\tcount\texpect\tmax.err\terror counts"
## [83] "5\t2\t12.1\t0\t2"
## [84] ""
## [85] ""
## [86] "=== Second read: Adapter 4 ==="
## [87] ""
## [88] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 546 times"
## [89] ""
## [90] "No. of allowed errors:"
## [91] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [92] ""
## [93] "Bases preceding removed adapters:"
## [94] " A: 81.1%"
## [95] " C: 12.8%"
## [96] " G: 2.2%"
## [97] " T: 3.8%"
## [98] " none/other: 0.0%"
## [99] "WARNING:"
## [100] " The adapter is preceded by \"A\" extremely often."
## [101] " The provided adapter sequence could be incomplete at its 3' end."
## [102] ""
## [103] "Overview of removed sequences"
## [104] "length\tcount\texpect\tmax.err\terror counts"
## [105] "5\t4\t12.1\t0\t4"
## [106] "6\t4\t3.0\t0\t4"
## [107] "7\t5\t0.8\t0\t5"
## [108] "8\t4\t0.2\t0\t4"
## [109] "9\t4\t0.0\t0\t4"
## [110] "10\t3\t0.0\t1\t3"
## [111] "11\t2\t0.0\t1\t1 1"
## [112] "12\t4\t0.0\t1\t3 1"
## [113] "13\t1\t0.0\t1\t0 1"
## [114] "14\t8\t0.0\t1\t7 1"
## [115] "15\t3\t0.0\t1\t3"
## [116] "16\t9\t0.0\t1\t8 1"
## [117] "17\t3\t0.0\t1\t3"
## [118] "18\t3\t0.0\t1\t1 2"
## [119] "19\t3\t0.0\t1\t1 2"
## [120] "20\t7\t0.0\t2\t7"
## [121] "21\t4\t0.0\t2\t4"
## [122] "22\t4\t0.0\t2\t3 1"
## [123] "23\t3\t0.0\t2\t3"
## [124] "24\t2\t0.0\t2\t2"
## [125] "25\t8\t0.0\t2\t7 1"
## [126] "26\t2\t0.0\t2\t1 0 1"
## [127] "27\t5\t0.0\t2\t3 1 1"
## [128] "28\t3\t0.0\t2\t2 1"
## [129] "29\t2\t0.0\t2\t2"
## [130] "30\t4\t0.0\t3\t3 0 1"
## [131] "31\t6\t0.0\t3\t4 2"
## [132] "32\t4\t0.0\t3\t4"
## [133] "33\t8\t0.0\t3\t5 2 0 1"
## [134] "34\t7\t0.0\t3\t5 1 1"
## [135] "35\t6\t0.0\t3\t4 2"
## [136] "36\t5\t0.0\t3\t4 1"
## [137] "37\t1\t0.0\t3\t0 1"
## [138] "38\t2\t0.0\t3\t2"
## [139] "39\t5\t0.0\t3\t2 3"
## [140] "40\t4\t0.0\t4\t3 0 1"
## [141] "41\t2\t0.0\t4\t1 0 1"
## [142] "42\t5\t0.0\t4\t4 0 0 1"
## [143] "43\t5\t0.0\t4\t4 1"
## [144] "44\t2\t0.0\t4\t2"
## [145] "45\t5\t0.0\t4\t2 1 2"
## [146] "46\t8\t0.0\t4\t8"
## [147] "47\t4\t0.0\t4\t4"
## [148] "48\t2\t0.0\t4\t2"
## [149] "49\t1\t0.0\t4\t0 1"
## [150] "50\t7\t0.0\t4\t6 1"
## [151] "51\t5\t0.0\t4\t4 1"
## [152] "52\t13\t0.0\t4\t10 3"
## [153] "53\t3\t0.0\t4\t3"
## [154] "54\t5\t0.0\t4\t5"
## [155] "55\t4\t0.0\t4\t2 1 1"
## [156] "56\t1\t0.0\t4\t0 1"
## [157] "57\t5\t0.0\t4\t4 0 1"
## [158] "58\t6\t0.0\t4\t4 0 1 1"
## [159] "59\t2\t0.0\t4\t2"
## [160] "60\t2\t0.0\t4\t2"
## [161] "61\t6\t0.0\t4\t5 0 0 1"
## [162] "62\t3\t0.0\t4\t1 1 1"
## [163] "63\t5\t0.0\t4\t4 1"
## [164] "64\t10\t0.0\t4\t9 1"
## [165] "65\t4\t0.0\t4\t4"
## [166] "66\t2\t0.0\t4\t0 1 0 0 1"
## [167] "67\t2\t0.0\t4\t2"
## [168] "68\t3\t0.0\t4\t3"
## [169] "69\t1\t0.0\t4\t1"
## [170] "70\t1\t0.0\t4\t1"
## [171] "71\t4\t0.0\t4\t4"
## [172] "72\t8\t0.0\t4\t8"
## [173] "73\t6\t0.0\t4\t2 4"
## [174] "74\t7\t0.0\t4\t7"
## [175] "75\t6\t0.0\t4\t6"
## [176] "76\t1\t0.0\t4\t1"
## [177] "77\t4\t0.0\t4\t4"
## [178] "78\t1\t0.0\t4\t1"
## [179] "79\t6\t0.0\t4\t5 0 1"
## [180] "80\t2\t0.0\t4\t2"
## [181] "81\t5\t0.0\t4\t4 1"
## [182] "82\t2\t0.0\t4\t2"
## [183] "83\t2\t0.0\t4\t2"
## [184] "84\t4\t0.0\t4\t3 1"
## [185] "85\t7\t0.0\t4\t6 0 1"
## [186] "86\t10\t0.0\t4\t10"
## [187] "87\t6\t0.0\t4\t6"
## [188] "88\t2\t0.0\t4\t1 1"
## [189] "89\t6\t0.0\t4\t6"
## [190] "90\t2\t0.0\t4\t2"
## [191] "91\t3\t0.0\t4\t3"
## [192] "92\t7\t0.0\t4\t6 1"
## [193] "93\t2\t0.0\t4\t2"
## [194] "94\t8\t0.0\t4\t7 0 1"
## [195] "95\t6\t0.0\t4\t5 1"
## [196] "96\t8\t0.0\t4\t5 3"
## [197] "97\t8\t0.0\t4\t7 0 1"
## [198] "99\t4\t0.0\t4\t4"
## [199] "100\t4\t0.0\t4\t2 1 0 1"
## [200] "101\t2\t0.0\t4\t2"
## [201] "102\t3\t0.0\t4\t3"
## [202] "103\t3\t0.0\t4\t3"
## [203] "104\t9\t0.0\t4\t9"
## [204] "105\t24\t0.0\t4\t24"
## [205] "106\t3\t0.0\t4\t2 1"
## [206] "107\t3\t0.0\t4\t2 1"
## [207] "108\t3\t0.0\t4\t3"
## [208] "109\t2\t0.0\t4\t1 1"
## [209] "110\t9\t0.0\t4\t7 2"
## [210] "111\t4\t0.0\t4\t4"
## [211] "112\t3\t0.0\t4\t3"
## [212] "113\t2\t0.0\t4\t2"
## [213] "115\t1\t0.0\t4\t1"
## [214] "117\t2\t0.0\t4\t2"
## [215] "118\t10\t0.0\t4\t8 2"
## [216] "119\t1\t0.0\t4\t1"
## [217] "120\t3\t0.0\t4\t3"
## [218] "121\t1\t0.0\t4\t1"
## [219] "122\t1\t0.0\t4\t1"
## [220] "125\t3\t0.0\t4\t3"
## [221] "126\t3\t0.0\t4\t3"
## [222] "127\t4\t0.0\t4\t2 2"
## [223] "128\t2\t0.0\t4\t1 0 1"
## [224] "129\t1\t0.0\t4\t0 1"
## [225] "130\t1\t0.0\t4\t1"
## [226] "132\t1\t0.0\t4\t1"
## [227] "134\t2\t0.0\t4\t1 1"
## [228] "139\t1\t0.0\t4\t1"
## [229] "142\t1\t0.0\t4\t1"
## [230] "144\t3\t0.0\t4\t3"
## [231] "145\t3\t0.0\t4\t0 0 3"
## [232] "146\t1\t0.0\t4\t1"
## [233] "154\t1\t0.0\t4\t1"
## [234] "156\t2\t0.0\t4\t2"
## [235] "159\t1\t0.0\t4\t1"
## [236] "160\t4\t0.0\t4\t4"
## [237] "161\t1\t0.0\t4\t1"
## [238] "163\t1\t0.0\t4\t1"
## [239] "164\t1\t0.0\t4\t1"
## [240] "166\t1\t0.0\t4\t1"
## [241] "167\t1\t0.0\t4\t0 1"
## [242] "183\t1\t0.0\t4\t0 0 1"
## [243] ""
## [244] ""
## [245] "WARNING:"
## [246] " One or more of your adapter sequences may be incomplete."
## [247] " Please see the detailed output above."
##
## [[8]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/104RNA3_S8_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/104RNA3_S8_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/104RNA3_S8_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/104RNA3_S8_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.68 s (117 us/read; 0.51 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 14,346"
## [9] " Read 1 with adapter: 23 (0.2%)"
## [10] " Read 2 with adapter: 456 (3.2%)"
## [11] "Pairs written (passing filters): 14,346 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 6,025,320 bp"
## [14] " Read 1: 2,811,816 bp"
## [15] " Read 2: 3,213,504 bp"
## [16] "Total written (filtered): 5,991,740 bp (99.4%)"
## [17] " Read 1: 2,810,762 bp"
## [18] " Read 2: 3,180,978 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 4 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "8\t1\t0.2\t0\t1"
## [30] "17\t2\t0.0\t1\t2"
## [31] "37\t1\t0.0\t3\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 19 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 36.8%"
## [43] " C: 0.0%"
## [44] " G: 63.2%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "5\t1\t14.0\t0\t1"
## [51] "8\t1\t0.2\t0\t1"
## [52] "9\t1\t0.1\t0\t1"
## [53] "12\t1\t0.0\t1\t1"
## [54] "17\t2\t0.0\t1\t2"
## [55] "36\t3\t0.0\t2\t3"
## [56] "56\t1\t0.0\t2\t1"
## [57] "71\t1\t0.0\t2\t1"
## [58] "73\t1\t0.0\t2\t1"
## [59] "75\t1\t0.0\t2\t1"
## [60] "81\t1\t0.0\t2\t1"
## [61] "82\t1\t0.0\t2\t1"
## [62] "90\t3\t0.0\t2\t3"
## [63] "91\t1\t0.0\t2\t1"
## [64] ""
## [65] ""
## [66] "=== Second read: Adapter 3 ==="
## [67] ""
## [68] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [69] ""
## [70] "No. of allowed errors:"
## [71] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [72] ""
## [73] "Overview of removed sequences"
## [74] "length\tcount\texpect\tmax.err\terror counts"
## [75] "92\t1\t0.0\t2\t1"
## [76] ""
## [77] ""
## [78] "=== Second read: Adapter 4 ==="
## [79] ""
## [80] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 456 times"
## [81] ""
## [82] "No. of allowed errors:"
## [83] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [84] ""
## [85] "Bases preceding removed adapters:"
## [86] " A: 86.4%"
## [87] " C: 10.5%"
## [88] " G: 1.5%"
## [89] " T: 1.5%"
## [90] " none/other: 0.0%"
## [91] "WARNING:"
## [92] " The adapter is preceded by \"A\" extremely often."
## [93] " The provided adapter sequence could be incomplete at its 3' end."
## [94] ""
## [95] "Overview of removed sequences"
## [96] "length\tcount\texpect\tmax.err\terror counts"
## [97] "5\t6\t14.0\t0\t6"
## [98] "6\t6\t3.5\t0\t6"
## [99] "7\t1\t0.9\t0\t1"
## [100] "8\t4\t0.2\t0\t4"
## [101] "9\t1\t0.1\t0\t1"
## [102] "10\t1\t0.0\t1\t1"
## [103] "11\t2\t0.0\t1\t1 1"
## [104] "12\t2\t0.0\t1\t1 1"
## [105] "14\t6\t0.0\t1\t5 1"
## [106] "15\t3\t0.0\t1\t3"
## [107] "16\t2\t0.0\t1\t2"
## [108] "17\t2\t0.0\t1\t1 1"
## [109] "18\t1\t0.0\t1\t1"
## [110] "19\t2\t0.0\t1\t1 1"
## [111] "20\t1\t0.0\t2\t1"
## [112] "21\t2\t0.0\t2\t2"
## [113] "22\t6\t0.0\t2\t4 2"
## [114] "23\t5\t0.0\t2\t2 2 1"
## [115] "24\t4\t0.0\t2\t3 1"
## [116] "25\t4\t0.0\t2\t2 1 1"
## [117] "26\t1\t0.0\t2\t0 0 1"
## [118] "27\t5\t0.0\t2\t5"
## [119] "29\t1\t0.0\t2\t0 1"
## [120] "30\t1\t0.0\t3\t0 0 1"
## [121] "31\t1\t0.0\t3\t1"
## [122] "32\t5\t0.0\t3\t3 2"
## [123] "33\t3\t0.0\t3\t3"
## [124] "34\t3\t0.0\t3\t2 0 0 1"
## [125] "35\t4\t0.0\t3\t4"
## [126] "36\t3\t0.0\t3\t3"
## [127] "37\t2\t0.0\t3\t2"
## [128] "38\t2\t0.0\t3\t0 2"
## [129] "39\t3\t0.0\t3\t3"
## [130] "40\t4\t0.0\t4\t2 2"
## [131] "41\t9\t0.0\t4\t8 1"
## [132] "42\t5\t0.0\t4\t4 1"
## [133] "43\t6\t0.0\t4\t5 1"
## [134] "44\t3\t0.0\t4\t2 1"
## [135] "45\t5\t0.0\t4\t3 2"
## [136] "46\t10\t0.0\t4\t5 1 2 0 2"
## [137] "47\t3\t0.0\t4\t3"
## [138] "48\t1\t0.0\t4\t1"
## [139] "49\t1\t0.0\t4\t0 0 1"
## [140] "50\t4\t0.0\t4\t3 0 0 1"
## [141] "51\t8\t0.0\t4\t6 2"
## [142] "52\t12\t0.0\t4\t10 2"
## [143] "53\t3\t0.0\t4\t3"
## [144] "54\t2\t0.0\t4\t2"
## [145] "55\t1\t0.0\t4\t0 1"
## [146] "56\t5\t0.0\t4\t4 1"
## [147] "57\t3\t0.0\t4\t3"
## [148] "58\t6\t0.0\t4\t4 2"
## [149] "59\t4\t0.0\t4\t4"
## [150] "60\t3\t0.0\t4\t3"
## [151] "61\t5\t0.0\t4\t5"
## [152] "62\t7\t0.0\t4\t7"
## [153] "63\t5\t0.0\t4\t4 1"
## [154] "64\t9\t0.0\t4\t6 2 0 1"
## [155] "65\t4\t0.0\t4\t3 1"
## [156] "66\t6\t0.0\t4\t5 1"
## [157] "67\t1\t0.0\t4\t0 0 1"
## [158] "68\t3\t0.0\t4\t1 2"
## [159] "69\t2\t0.0\t4\t1 1"
## [160] "70\t3\t0.0\t4\t2 1"
## [161] "71\t3\t0.0\t4\t3"
## [162] "72\t6\t0.0\t4\t6"
## [163] "73\t4\t0.0\t4\t2 2"
## [164] "74\t3\t0.0\t4\t3"
## [165] "75\t7\t0.0\t4\t7"
## [166] "76\t3\t0.0\t4\t3"
## [167] "77\t2\t0.0\t4\t1 1"
## [168] "78\t1\t0.0\t4\t1"
## [169] "79\t9\t0.0\t4\t8 1"
## [170] "80\t1\t0.0\t4\t1"
## [171] "81\t2\t0.0\t4\t1 0 1"
## [172] "82\t2\t0.0\t4\t2"
## [173] "83\t1\t0.0\t4\t0 1"
## [174] "84\t5\t0.0\t4\t4 1"
## [175] "85\t9\t0.0\t4\t6 2 1"
## [176] "86\t9\t0.0\t4\t9"
## [177] "87\t6\t0.0\t4\t5 0 1"
## [178] "88\t5\t0.0\t4\t4 0 0 1"
## [179] "89\t2\t0.0\t4\t2"
## [180] "90\t1\t0.0\t4\t1"
## [181] "91\t1\t0.0\t4\t0 1"
## [182] "92\t5\t0.0\t4\t5"
## [183] "93\t3\t0.0\t4\t2 1"
## [184] "94\t6\t0.0\t4\t5 1"
## [185] "95\t4\t0.0\t4\t4"
## [186] "96\t4\t0.0\t4\t3 1"
## [187] "97\t1\t0.0\t4\t1"
## [188] "99\t2\t0.0\t4\t1 1"
## [189] "100\t1\t0.0\t4\t1"
## [190] "101\t2\t0.0\t4\t2"
## [191] "102\t4\t0.0\t4\t4"
## [192] "103\t2\t0.0\t4\t2"
## [193] "104\t3\t0.0\t4\t2 0 1"
## [194] "105\t4\t0.0\t4\t4"
## [195] "107\t3\t0.0\t4\t3"
## [196] "108\t2\t0.0\t4\t2"
## [197] "109\t1\t0.0\t4\t0 1"
## [198] "110\t1\t0.0\t4\t1"
## [199] "111\t7\t0.0\t4\t6 1"
## [200] "112\t4\t0.0\t4\t4"
## [201] "113\t2\t0.0\t4\t1 1"
## [202] "114\t4\t0.0\t4\t3 0 1"
## [203] "115\t3\t0.0\t4\t3"
## [204] "116\t3\t0.0\t4\t2 1"
## [205] "117\t4\t0.0\t4\t4"
## [206] "118\t9\t0.0\t4\t9"
## [207] "119\t6\t0.0\t4\t5 1"
## [208] "120\t2\t0.0\t4\t2"
## [209] "121\t2\t0.0\t4\t2"
## [210] "123\t1\t0.0\t4\t1"
## [211] "124\t2\t0.0\t4\t2"
## [212] "125\t2\t0.0\t4\t2"
## [213] "126\t1\t0.0\t4\t1"
## [214] "127\t3\t0.0\t4\t2 1"
## [215] "129\t1\t0.0\t4\t1"
## [216] "130\t4\t0.0\t4\t4"
## [217] "132\t1\t0.0\t4\t1"
## [218] "133\t2\t0.0\t4\t2"
## [219] "134\t2\t0.0\t4\t2"
## [220] "139\t1\t0.0\t4\t1"
## [221] "140\t3\t0.0\t4\t2 1"
## [222] "141\t1\t0.0\t4\t1"
## [223] "142\t1\t0.0\t4\t1"
## [224] "146\t3\t0.0\t4\t3"
## [225] "149\t1\t0.0\t4\t1"
## [226] "150\t1\t0.0\t4\t1"
## [227] "152\t1\t0.0\t4\t1"
## [228] "154\t1\t0.0\t4\t1"
## [229] "158\t1\t0.0\t4\t1"
## [230] "159\t2\t0.0\t4\t2"
## [231] "160\t4\t0.0\t4\t4"
## [232] "161\t2\t0.0\t4\t2"
## [233] "173\t1\t0.0\t4\t1"
## [234] ""
## [235] ""
## [236] "WARNING:"
## [237] " One or more of your adapter sequences may be incomplete."
## [238] " Please see the detailed output above."
##
## [[9]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1051_S9_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1051_S9_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1051_S9_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1051_S9_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.66 s (113 us/read; 0.53 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 14,658"
## [9] " Read 1 with adapter: 4 (0.0%)"
## [10] " Read 2 with adapter: 127 (0.9%)"
## [11] "Pairs written (passing filters): 14,658 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 6,156,360 bp"
## [14] " Read 1: 2,872,968 bp"
## [15] " Read 2: 3,283,392 bp"
## [16] "Total written (filtered): 6,147,694 bp (99.9%)"
## [17] " Read 1: 2,872,872 bp"
## [18] " Read 2: 3,274,822 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t14.3\t0\t1"
## [30] "7\t1\t0.9\t0\t1"
## [31] "14\t1\t0.0\t1\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 1 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 0.0%"
## [43] " C: 100.0%"
## [44] " G: 0.0%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "70\t1\t0.0\t2\t1"
## [51] ""
## [52] ""
## [53] "=== Second read: Adapter 3 ==="
## [54] ""
## [55] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 2 times"
## [56] ""
## [57] "No. of allowed errors:"
## [58] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [59] ""
## [60] "Overview of removed sequences"
## [61] "length\tcount\texpect\tmax.err\terror counts"
## [62] "9\t1\t0.1\t0\t1"
## [63] "24\t1\t0.0\t2\t1"
## [64] ""
## [65] ""
## [66] "=== Second read: Adapter 4 ==="
## [67] ""
## [68] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 125 times"
## [69] ""
## [70] "No. of allowed errors:"
## [71] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [72] ""
## [73] "Bases preceding removed adapters:"
## [74] " A: 82.4%"
## [75] " C: 11.2%"
## [76] " G: 4.8%"
## [77] " T: 1.6%"
## [78] " none/other: 0.0%"
## [79] "WARNING:"
## [80] " The adapter is preceded by \"A\" extremely often."
## [81] " The provided adapter sequence could be incomplete at its 3' end."
## [82] ""
## [83] "Overview of removed sequences"
## [84] "length\tcount\texpect\tmax.err\terror counts"
## [85] "5\t10\t14.3\t0\t10"
## [86] "6\t2\t3.6\t0\t2"
## [87] "8\t2\t0.2\t0\t2"
## [88] "10\t2\t0.0\t1\t2"
## [89] "11\t1\t0.0\t1\t1"
## [90] "16\t4\t0.0\t1\t4"
## [91] "21\t1\t0.0\t2\t1"
## [92] "23\t1\t0.0\t2\t1"
## [93] "24\t1\t0.0\t2\t1"
## [94] "25\t1\t0.0\t2\t1"
## [95] "27\t2\t0.0\t2\t2"
## [96] "29\t1\t0.0\t2\t1"
## [97] "30\t1\t0.0\t3\t0 0 1"
## [98] "31\t3\t0.0\t3\t1 0 2"
## [99] "32\t1\t0.0\t3\t0 1"
## [100] "33\t4\t0.0\t3\t1 3"
## [101] "34\t1\t0.0\t3\t0 0 1"
## [102] "35\t1\t0.0\t3\t0 1"
## [103] "37\t2\t0.0\t3\t2"
## [104] "39\t1\t0.0\t3\t1"
## [105] "40\t1\t0.0\t4\t1"
## [106] "44\t1\t0.0\t4\t1"
## [107] "45\t3\t0.0\t4\t1 1 1"
## [108] "46\t2\t0.0\t4\t2"
## [109] "48\t2\t0.0\t4\t2"
## [110] "51\t1\t0.0\t4\t1"
## [111] "52\t1\t0.0\t4\t1"
## [112] "57\t1\t0.0\t4\t0 1"
## [113] "59\t2\t0.0\t4\t2"
## [114] "61\t2\t0.0\t4\t2"
## [115] "62\t1\t0.0\t4\t1"
## [116] "63\t3\t0.0\t4\t3"
## [117] "64\t3\t0.0\t4\t3"
## [118] "65\t1\t0.0\t4\t1"
## [119] "66\t2\t0.0\t4\t1 1"
## [120] "68\t1\t0.0\t4\t1"
## [121] "70\t2\t0.0\t4\t2"
## [122] "71\t2\t0.0\t4\t2"
## [123] "72\t1\t0.0\t4\t1"
## [124] "77\t1\t0.0\t4\t1"
## [125] "79\t1\t0.0\t4\t1"
## [126] "80\t1\t0.0\t4\t1"
## [127] "82\t3\t0.0\t4\t2 1"
## [128] "84\t1\t0.0\t4\t1"
## [129] "86\t2\t0.0\t4\t2"
## [130] "88\t1\t0.0\t4\t1"
## [131] "89\t1\t0.0\t4\t1"
## [132] "92\t1\t0.0\t4\t1"
## [133] "93\t2\t0.0\t4\t2"
## [134] "94\t1\t0.0\t4\t1"
## [135] "97\t1\t0.0\t4\t1"
## [136] "98\t2\t0.0\t4\t1 0 1"
## [137] "102\t1\t0.0\t4\t1"
## [138] "105\t2\t0.0\t4\t2"
## [139] "106\t2\t0.0\t4\t2"
## [140] "108\t1\t0.0\t4\t1"
## [141] "111\t2\t0.0\t4\t2"
## [142] "114\t1\t0.0\t4\t0 1"
## [143] "119\t1\t0.0\t4\t1"
## [144] "120\t1\t0.0\t4\t0 1"
## [145] "123\t1\t0.0\t4\t1"
## [146] "124\t1\t0.0\t4\t1"
## [147] "126\t5\t0.0\t4\t4 1"
## [148] "128\t1\t0.0\t4\t1"
## [149] "129\t2\t0.0\t4\t2"
## [150] "132\t1\t0.0\t4\t1"
## [151] "135\t1\t0.0\t4\t0 0 1"
## [152] "142\t1\t0.0\t4\t1"
## [153] "144\t1\t0.0\t4\t1"
## [154] "146\t1\t0.0\t4\t1"
## [155] "148\t1\t0.0\t4\t1"
## [156] "149\t1\t0.0\t4\t1"
## [157] "150\t1\t0.0\t4\t0 0 0 1"
## [158] "156\t1\t0.0\t4\t1"
## [159] "160\t1\t0.0\t4\t1"
## [160] "164\t1\t0.0\t4\t1"
## [161] "174\t1\t0.0\t4\t1"
## [162] ""
## [163] ""
## [164] "WARNING:"
## [165] " One or more of your adapter sequences may be incomplete."
## [166] " Please see the detailed output above."
##
## [[10]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1052_S10_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1052_S10_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1052_S10_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1052_S10_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.51 s (110 us/read; 0.55 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 13,743"
## [9] " Read 1 with adapter: 1 (0.0%)"
## [10] " Read 2 with adapter: 129 (0.9%)"
## [11] "Pairs written (passing filters): 13,742 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 5,772,060 bp"
## [14] " Read 1: 2,693,628 bp"
## [15] " Read 2: 3,078,432 bp"
## [16] "Total written (filtered): 5,764,252 bp (99.9%)"
## [17] " Read 1: 2,693,295 bp"
## [18] " Read 2: 3,070,957 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 1 times"
## [27] ""
## [28] "No. of allowed errors:"
## [29] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [30] ""
## [31] "Bases preceding removed adapters:"
## [32] " A: 100.0%"
## [33] " C: 0.0%"
## [34] " G: 0.0%"
## [35] " T: 0.0%"
## [36] " none/other: 0.0%"
## [37] ""
## [38] "Overview of removed sequences"
## [39] "length\tcount\texpect\tmax.err\terror counts"
## [40] "137\t1\t0.0\t2\t1"
## [41] ""
## [42] ""
## [43] "=== Second read: Adapter 3 ==="
## [44] ""
## [45] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [46] ""
## [47] "=== Second read: Adapter 4 ==="
## [48] ""
## [49] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 129 times"
## [50] ""
## [51] "No. of allowed errors:"
## [52] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [53] ""
## [54] "Bases preceding removed adapters:"
## [55] " A: 79.1%"
## [56] " C: 15.5%"
## [57] " G: 3.9%"
## [58] " T: 1.6%"
## [59] " none/other: 0.0%"
## [60] ""
## [61] "Overview of removed sequences"
## [62] "length\tcount\texpect\tmax.err\terror counts"
## [63] "5\t11\t13.4\t0\t11"
## [64] "6\t1\t3.4\t0\t1"
## [65] "7\t2\t0.8\t0\t2"
## [66] "8\t2\t0.2\t0\t2"
## [67] "9\t2\t0.1\t0\t2"
## [68] "10\t1\t0.0\t1\t0 1"
## [69] "12\t1\t0.0\t1\t1"
## [70] "13\t3\t0.0\t1\t3"
## [71] "14\t2\t0.0\t1\t2"
## [72] "15\t1\t0.0\t1\t1"
## [73] "16\t4\t0.0\t1\t4"
## [74] "17\t2\t0.0\t1\t1 1"
## [75] "19\t1\t0.0\t1\t1"
## [76] "20\t2\t0.0\t2\t1 1"
## [77] "22\t1\t0.0\t2\t1"
## [78] "24\t2\t0.0\t2\t2"
## [79] "25\t1\t0.0\t2\t1"
## [80] "26\t1\t0.0\t2\t0 1"
## [81] "29\t2\t0.0\t2\t1 1"
## [82] "30\t1\t0.0\t3\t0 1"
## [83] "31\t1\t0.0\t3\t1"
## [84] "32\t3\t0.0\t3\t3"
## [85] "33\t2\t0.0\t3\t2"
## [86] "34\t2\t0.0\t3\t1 1"
## [87] "35\t3\t0.0\t3\t3"
## [88] "37\t1\t0.0\t3\t1"
## [89] "38\t1\t0.0\t3\t0 0 1"
## [90] "42\t3\t0.0\t4\t1 0 1 1"
## [91] "43\t1\t0.0\t4\t1"
## [92] "44\t2\t0.0\t4\t2"
## [93] "45\t1\t0.0\t4\t1"
## [94] "47\t2\t0.0\t4\t1 0 0 1"
## [95] "48\t1\t0.0\t4\t1"
## [96] "51\t1\t0.0\t4\t0 1"
## [97] "52\t1\t0.0\t4\t1"
## [98] "53\t1\t0.0\t4\t1"
## [99] "57\t2\t0.0\t4\t2"
## [100] "58\t2\t0.0\t4\t2"
## [101] "59\t1\t0.0\t4\t1"
## [102] "64\t2\t0.0\t4\t1 1"
## [103] "65\t3\t0.0\t4\t3"
## [104] "69\t1\t0.0\t4\t1"
## [105] "72\t1\t0.0\t4\t1"
## [106] "73\t1\t0.0\t4\t1"
## [107] "78\t1\t0.0\t4\t1"
## [108] "79\t1\t0.0\t4\t1"
## [109] "82\t2\t0.0\t4\t2"
## [110] "85\t3\t0.0\t4\t3"
## [111] "86\t5\t0.0\t4\t4 1"
## [112] "87\t3\t0.0\t4\t1 1 0 1"
## [113] "88\t2\t0.0\t4\t1 0 1"
## [114] "91\t1\t0.0\t4\t1"
## [115] "94\t2\t0.0\t4\t2"
## [116] "98\t2\t0.0\t4\t2"
## [117] "101\t1\t0.0\t4\t1"
## [118] "104\t2\t0.0\t4\t1 1"
## [119] "105\t3\t0.0\t4\t3"
## [120] "106\t1\t0.0\t4\t1"
## [121] "108\t2\t0.0\t4\t2"
## [122] "109\t1\t0.0\t4\t1"
## [123] "111\t1\t0.0\t4\t1"
## [124] "118\t1\t0.0\t4\t1"
## [125] "120\t1\t0.0\t4\t1"
## [126] "121\t2\t0.0\t4\t1 1"
## [127] "128\t1\t0.0\t4\t1"
## [128] "130\t1\t0.0\t4\t1"
## [129] "135\t1\t0.0\t4\t1"
## [130] "139\t1\t0.0\t4\t1"
## [131] "140\t2\t0.0\t4\t2"
## [132] "142\t1\t0.0\t4\t1"
## [133] "143\t1\t0.0\t4\t1"
## [134] "144\t1\t0.0\t4\t1"
## [135] "180\t1\t0.0\t4\t1"
##
## [[11]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1053_S11_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1053_S11_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1053_S11_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1053_S11_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.23 s (112 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 10,965"
## [9] " Read 1 with adapter: 6 (0.1%)"
## [10] " Read 2 with adapter: 90 (0.8%)"
## [11] "Pairs written (passing filters): 10,965 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 4,605,300 bp"
## [14] " Read 1: 2,149,140 bp"
## [15] " Read 2: 2,456,160 bp"
## [16] "Total written (filtered): 4,599,637 bp (99.9%)"
## [17] " Read 1: 2,148,747 bp"
## [18] " Read 2: 2,450,890 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 2 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "8\t1\t0.2\t0\t1"
## [30] "28\t1\t0.0\t2\t1"
## [31] ""
## [32] ""
## [33] "=== First read: Adapter 2 ==="
## [34] ""
## [35] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 4 times"
## [36] ""
## [37] "No. of allowed errors:"
## [38] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [39] ""
## [40] "Bases preceding removed adapters:"
## [41] " A: 0.0%"
## [42] " C: 0.0%"
## [43] " G: 100.0%"
## [44] " T: 0.0%"
## [45] " none/other: 0.0%"
## [46] ""
## [47] "Overview of removed sequences"
## [48] "length\tcount\texpect\tmax.err\terror counts"
## [49] "34\t1\t0.0\t2\t0 1"
## [50] "41\t1\t0.0\t2\t1"
## [51] "141\t2\t0.0\t2\t2"
## [52] ""
## [53] ""
## [54] "=== Second read: Adapter 3 ==="
## [55] ""
## [56] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [57] ""
## [58] "No. of allowed errors:"
## [59] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [60] ""
## [61] "Overview of removed sequences"
## [62] "length\tcount\texpect\tmax.err\terror counts"
## [63] "73\t1\t0.0\t2\t1"
## [64] ""
## [65] ""
## [66] "=== Second read: Adapter 4 ==="
## [67] ""
## [68] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 89 times"
## [69] ""
## [70] "No. of allowed errors:"
## [71] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [72] ""
## [73] "Bases preceding removed adapters:"
## [74] " A: 86.5%"
## [75] " C: 6.7%"
## [76] " G: 4.5%"
## [77] " T: 2.2%"
## [78] " none/other: 0.0%"
## [79] "WARNING:"
## [80] " The adapter is preceded by \"A\" extremely often."
## [81] " The provided adapter sequence could be incomplete at its 3' end."
## [82] ""
## [83] "Overview of removed sequences"
## [84] "length\tcount\texpect\tmax.err\terror counts"
## [85] "5\t7\t10.7\t0\t7"
## [86] "6\t1\t2.7\t0\t1"
## [87] "8\t1\t0.2\t0\t1"
## [88] "9\t1\t0.0\t0\t1"
## [89] "11\t1\t0.0\t1\t0 1"
## [90] "12\t2\t0.0\t1\t2"
## [91] "13\t1\t0.0\t1\t0 1"
## [92] "16\t3\t0.0\t1\t2 1"
## [93] "20\t1\t0.0\t2\t1"
## [94] "22\t1\t0.0\t2\t1"
## [95] "30\t1\t0.0\t3\t0 1"
## [96] "31\t1\t0.0\t3\t1"
## [97] "32\t1\t0.0\t3\t0 1"
## [98] "33\t1\t0.0\t3\t1"
## [99] "34\t1\t0.0\t3\t1"
## [100] "35\t1\t0.0\t3\t1"
## [101] "36\t1\t0.0\t3\t1"
## [102] "39\t1\t0.0\t3\t1"
## [103] "40\t1\t0.0\t4\t0 1"
## [104] "41\t1\t0.0\t4\t0 1"
## [105] "42\t3\t0.0\t4\t3"
## [106] "43\t1\t0.0\t4\t1"
## [107] "44\t1\t0.0\t4\t1"
## [108] "46\t2\t0.0\t4\t2"
## [109] "48\t1\t0.0\t4\t1"
## [110] "51\t2\t0.0\t4\t2"
## [111] "52\t2\t0.0\t4\t2"
## [112] "53\t2\t0.0\t4\t2"
## [113] "55\t1\t0.0\t4\t1"
## [114] "56\t2\t0.0\t4\t1 0 0 0 1"
## [115] "57\t1\t0.0\t4\t1"
## [116] "58\t1\t0.0\t4\t1"
## [117] "62\t1\t0.0\t4\t0 1"
## [118] "63\t4\t0.0\t4\t4"
## [119] "64\t1\t0.0\t4\t1"
## [120] "68\t1\t0.0\t4\t1"
## [121] "71\t2\t0.0\t4\t2"
## [122] "72\t2\t0.0\t4\t1 1"
## [123] "73\t1\t0.0\t4\t1"
## [124] "74\t2\t0.0\t4\t0 1 1"
## [125] "77\t1\t0.0\t4\t1"
## [126] "78\t1\t0.0\t4\t1"
## [127] "79\t1\t0.0\t4\t1"
## [128] "81\t1\t0.0\t4\t1"
## [129] "83\t1\t0.0\t4\t1"
## [130] "84\t1\t0.0\t4\t1"
## [131] "85\t1\t0.0\t4\t1"
## [132] "86\t1\t0.0\t4\t1"
## [133] "90\t1\t0.0\t4\t0 1"
## [134] "91\t1\t0.0\t4\t0 1"
## [135] "94\t1\t0.0\t4\t0 1"
## [136] "99\t1\t0.0\t4\t1"
## [137] "100\t1\t0.0\t4\t1"
## [138] "102\t2\t0.0\t4\t2"
## [139] "103\t2\t0.0\t4\t2"
## [140] "106\t1\t0.0\t4\t1"
## [141] "107\t1\t0.0\t4\t1"
## [142] "113\t1\t0.0\t4\t1"
## [143] "116\t1\t0.0\t4\t1"
## [144] "118\t1\t0.0\t4\t1"
## [145] "122\t1\t0.0\t4\t1"
## [146] "129\t3\t0.0\t4\t3"
## [147] "144\t1\t0.0\t4\t1"
## [148] ""
## [149] ""
## [150] "WARNING:"
## [151] " One or more of your adapter sequences may be incomplete."
## [152] " Please see the detailed output above."
##
## [[12]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/105RNA1_S12_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/105RNA1_S12_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/105RNA1_S12_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/105RNA1_S12_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.68 s (105 us/read; 0.57 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 6,497"
## [9] " Read 1 with adapter: 21 (0.3%)"
## [10] " Read 2 with adapter: 134 (2.1%)"
## [11] "Pairs written (passing filters): 6,497 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 2,728,740 bp"
## [14] " Read 1: 1,273,412 bp"
## [15] " Read 2: 1,455,328 bp"
## [16] "Total written (filtered): 2,719,072 bp (99.6%)"
## [17] " Read 1: 1,272,441 bp"
## [18] " Read 2: 1,446,631 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 1 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "10\t1\t0.0\t1\t1"
## [30] ""
## [31] ""
## [32] "=== First read: Adapter 2 ==="
## [33] ""
## [34] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 20 times"
## [35] ""
## [36] "No. of allowed errors:"
## [37] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [38] ""
## [39] "Bases preceding removed adapters:"
## [40] " A: 20.0%"
## [41] " C: 0.0%"
## [42] " G: 80.0%"
## [43] " T: 0.0%"
## [44] " none/other: 0.0%"
## [45] ""
## [46] "Overview of removed sequences"
## [47] "length\tcount\texpect\tmax.err\terror counts"
## [48] "8\t1\t0.1\t0\t1"
## [49] "10\t2\t0.0\t1\t2"
## [50] "15\t2\t0.0\t1\t2"
## [51] "17\t1\t0.0\t1\t1"
## [52] "36\t6\t0.0\t2\t6"
## [53] "59\t1\t0.0\t2\t1"
## [54] "63\t1\t0.0\t2\t1"
## [55] "90\t5\t0.0\t2\t5"
## [56] "98\t1\t0.0\t2\t1"
## [57] ""
## [58] ""
## [59] "=== Second read: Adapter 3 ==="
## [60] ""
## [61] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [62] ""
## [63] "=== Second read: Adapter 4 ==="
## [64] ""
## [65] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 134 times"
## [66] ""
## [67] "No. of allowed errors:"
## [68] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [69] ""
## [70] "Bases preceding removed adapters:"
## [71] " A: 93.3%"
## [72] " C: 3.7%"
## [73] " G: 1.5%"
## [74] " T: 1.5%"
## [75] " none/other: 0.0%"
## [76] "WARNING:"
## [77] " The adapter is preceded by \"A\" extremely often."
## [78] " The provided adapter sequence could be incomplete at its 3' end."
## [79] ""
## [80] "Overview of removed sequences"
## [81] "length\tcount\texpect\tmax.err\terror counts"
## [82] "5\t6\t6.3\t0\t6"
## [83] "9\t1\t0.0\t0\t1"
## [84] "10\t1\t0.0\t1\t1"
## [85] "14\t1\t0.0\t1\t1"
## [86] "16\t4\t0.0\t1\t4"
## [87] "17\t1\t0.0\t1\t1"
## [88] "19\t1\t0.0\t1\t1"
## [89] "20\t1\t0.0\t2\t0 0 1"
## [90] "23\t3\t0.0\t2\t1 2"
## [91] "25\t2\t0.0\t2\t2"
## [92] "27\t1\t0.0\t2\t1"
## [93] "29\t2\t0.0\t2\t2"
## [94] "32\t1\t0.0\t3\t1"
## [95] "33\t1\t0.0\t3\t1"
## [96] "34\t2\t0.0\t3\t1 1"
## [97] "35\t4\t0.0\t3\t4"
## [98] "36\t3\t0.0\t3\t3"
## [99] "37\t1\t0.0\t3\t1"
## [100] "39\t1\t0.0\t3\t1"
## [101] "40\t2\t0.0\t4\t2"
## [102] "41\t1\t0.0\t4\t0 1"
## [103] "42\t1\t0.0\t4\t0 0 0 0 1"
## [104] "43\t4\t0.0\t4\t4"
## [105] "45\t2\t0.0\t4\t0 1 0 1"
## [106] "46\t2\t0.0\t4\t1 1"
## [107] "47\t2\t0.0\t4\t2"
## [108] "48\t1\t0.0\t4\t1"
## [109] "49\t1\t0.0\t4\t1"
## [110] "52\t4\t0.0\t4\t2 1 0 0 1"
## [111] "54\t1\t0.0\t4\t1"
## [112] "56\t1\t0.0\t4\t1"
## [113] "57\t1\t0.0\t4\t1"
## [114] "59\t2\t0.0\t4\t2"
## [115] "63\t4\t0.0\t4\t4"
## [116] "64\t6\t0.0\t4\t4 1 1"
## [117] "65\t1\t0.0\t4\t1"
## [118] "66\t1\t0.0\t4\t1"
## [119] "69\t1\t0.0\t4\t1"
## [120] "70\t1\t0.0\t4\t1"
## [121] "71\t2\t0.0\t4\t1 0 1"
## [122] "72\t3\t0.0\t4\t2 1"
## [123] "75\t1\t0.0\t4\t1"
## [124] "76\t1\t0.0\t4\t1"
## [125] "77\t1\t0.0\t4\t1"
## [126] "78\t2\t0.0\t4\t1 1"
## [127] "82\t1\t0.0\t4\t1"
## [128] "84\t2\t0.0\t4\t2"
## [129] "86\t5\t0.0\t4\t5"
## [130] "87\t2\t0.0\t4\t1 1"
## [131] "89\t1\t0.0\t4\t1"
## [132] "91\t1\t0.0\t4\t1"
## [133] "92\t1\t0.0\t4\t1"
## [134] "93\t1\t0.0\t4\t1"
## [135] "94\t4\t0.0\t4\t4"
## [136] "95\t1\t0.0\t4\t1"
## [137] "96\t2\t0.0\t4\t1 1"
## [138] "98\t1\t0.0\t4\t1"
## [139] "100\t1\t0.0\t4\t1"
## [140] "102\t1\t0.0\t4\t0 1"
## [141] "103\t1\t0.0\t4\t1"
## [142] "104\t3\t0.0\t4\t3"
## [143] "105\t1\t0.0\t4\t1"
## [144] "110\t1\t0.0\t4\t1"
## [145] "111\t2\t0.0\t4\t2"
## [146] "112\t1\t0.0\t4\t1"
## [147] "115\t1\t0.0\t4\t1"
## [148] "116\t1\t0.0\t4\t1"
## [149] "118\t5\t0.0\t4\t4 1"
## [150] "120\t2\t0.0\t4\t2"
## [151] "121\t1\t0.0\t4\t1"
## [152] "126\t2\t0.0\t4\t2"
## [153] "129\t1\t0.0\t4\t1"
## [154] "141\t1\t0.0\t4\t0 0 1"
## [155] "154\t1\t0.0\t4\t1"
## [156] ""
## [157] ""
## [158] "WARNING:"
## [159] " One or more of your adapter sequences may be incomplete."
## [160] " Please see the detailed output above."
##
## [[13]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/105RNA2_S13_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/105RNA2_S13_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/105RNA2_S13_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/105RNA2_S13_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.80 s (103 us/read; 0.58 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 7,754"
## [9] " Read 1 with adapter: 17 (0.2%)"
## [10] " Read 2 with adapter: 159 (2.1%)"
## [11] "Pairs written (passing filters): 7,753 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,256,680 bp"
## [14] " Read 1: 1,519,784 bp"
## [15] " Read 2: 1,736,896 bp"
## [16] "Total written (filtered): 3,245,708 bp (99.7%)"
## [17] " Read 1: 1,518,688 bp"
## [18] " Read 2: 1,727,020 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 17 times"
## [27] ""
## [28] "No. of allowed errors:"
## [29] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [30] ""
## [31] "Bases preceding removed adapters:"
## [32] " A: 47.1%"
## [33] " C: 0.0%"
## [34] " G: 52.9%"
## [35] " T: 0.0%"
## [36] " none/other: 0.0%"
## [37] ""
## [38] "Overview of removed sequences"
## [39] "length\tcount\texpect\tmax.err\terror counts"
## [40] "9\t2\t0.0\t0\t2"
## [41] "14\t1\t0.0\t1\t1"
## [42] "16\t1\t0.0\t1\t1"
## [43] "17\t3\t0.0\t1\t3"
## [44] "19\t1\t0.0\t1\t0 1"
## [45] "36\t3\t0.0\t2\t3"
## [46] "70\t1\t0.0\t2\t1"
## [47] "91\t1\t0.0\t2\t1"
## [48] "118\t2\t0.0\t2\t2"
## [49] "137\t1\t0.0\t2\t1"
## [50] "140\t1\t0.0\t2\t1"
## [51] ""
## [52] ""
## [53] "=== Second read: Adapter 3 ==="
## [54] ""
## [55] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [56] ""
## [57] "No. of allowed errors:"
## [58] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [59] ""
## [60] "Overview of removed sequences"
## [61] "length\tcount\texpect\tmax.err\terror counts"
## [62] "6\t1\t1.9\t0\t1"
## [63] ""
## [64] ""
## [65] "=== Second read: Adapter 4 ==="
## [66] ""
## [67] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 159 times"
## [68] ""
## [69] "No. of allowed errors:"
## [70] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [71] ""
## [72] "Bases preceding removed adapters:"
## [73] " A: 96.2%"
## [74] " C: 3.8%"
## [75] " G: 0.0%"
## [76] " T: 0.0%"
## [77] " none/other: 0.0%"
## [78] "WARNING:"
## [79] " The adapter is preceded by \"A\" extremely often."
## [80] " The provided adapter sequence could be incomplete at its 3' end."
## [81] ""
## [82] "Overview of removed sequences"
## [83] "length\tcount\texpect\tmax.err\terror counts"
## [84] "5\t2\t7.6\t0\t2"
## [85] "7\t1\t0.5\t0\t1"
## [86] "8\t1\t0.1\t0\t1"
## [87] "11\t1\t0.0\t1\t1"
## [88] "13\t1\t0.0\t1\t1"
## [89] "14\t2\t0.0\t1\t2"
## [90] "15\t2\t0.0\t1\t2"
## [91] "16\t2\t0.0\t1\t2"
## [92] "17\t2\t0.0\t1\t2"
## [93] "19\t4\t0.0\t1\t4"
## [94] "20\t1\t0.0\t2\t1"
## [95] "21\t1\t0.0\t2\t1"
## [96] "22\t1\t0.0\t2\t1"
## [97] "23\t1\t0.0\t2\t1"
## [98] "24\t2\t0.0\t2\t1 1"
## [99] "25\t3\t0.0\t2\t3"
## [100] "26\t1\t0.0\t2\t1"
## [101] "27\t1\t0.0\t2\t0 1"
## [102] "28\t1\t0.0\t2\t1"
## [103] "30\t3\t0.0\t3\t1 1 0 1"
## [104] "31\t1\t0.0\t3\t0 0 1"
## [105] "33\t2\t0.0\t3\t1 1"
## [106] "34\t5\t0.0\t3\t4 0 1"
## [107] "35\t4\t0.0\t3\t4"
## [108] "36\t2\t0.0\t3\t1 1"
## [109] "37\t3\t0.0\t3\t1 1 0 1"
## [110] "38\t2\t0.0\t3\t0 2"
## [111] "39\t1\t0.0\t3\t1"
## [112] "40\t3\t0.0\t4\t3"
## [113] "41\t2\t0.0\t4\t2"
## [114] "42\t2\t0.0\t4\t0 2"
## [115] "43\t1\t0.0\t4\t1"
## [116] "44\t3\t0.0\t4\t1 1 0 1"
## [117] "45\t6\t0.0\t4\t3 2 1"
## [118] "46\t2\t0.0\t4\t1 1"
## [119] "47\t1\t0.0\t4\t1"
## [120] "48\t4\t0.0\t4\t3 1"
## [121] "50\t1\t0.0\t4\t1"
## [122] "51\t1\t0.0\t4\t1"
## [123] "52\t4\t0.0\t4\t4"
## [124] "53\t2\t0.0\t4\t2"
## [125] "54\t1\t0.0\t4\t1"
## [126] "56\t1\t0.0\t4\t1"
## [127] "58\t3\t0.0\t4\t2 1"
## [128] "59\t2\t0.0\t4\t1 1"
## [129] "61\t1\t0.0\t4\t1"
## [130] "62\t1\t0.0\t4\t1"
## [131] "63\t1\t0.0\t4\t1"
## [132] "64\t6\t0.0\t4\t6"
## [133] "65\t1\t0.0\t4\t1"
## [134] "66\t1\t0.0\t4\t1"
## [135] "67\t1\t0.0\t4\t1"
## [136] "68\t1\t0.0\t4\t1"
## [137] "72\t3\t0.0\t4\t2 1"
## [138] "77\t1\t0.0\t4\t1"
## [139] "79\t3\t0.0\t4\t3"
## [140] "81\t1\t0.0\t4\t1"
## [141] "83\t2\t0.0\t4\t1 1"
## [142] "84\t2\t0.0\t4\t2"
## [143] "86\t1\t0.0\t4\t0 1"
## [144] "87\t1\t0.0\t4\t1"
## [145] "88\t1\t0.0\t4\t0 1"
## [146] "90\t1\t0.0\t4\t1"
## [147] "91\t1\t0.0\t4\t1"
## [148] "94\t4\t0.0\t4\t4"
## [149] "96\t2\t0.0\t4\t1 1"
## [150] "98\t1\t0.0\t4\t1"
## [151] "99\t1\t0.0\t4\t1"
## [152] "104\t2\t0.0\t4\t1 1"
## [153] "105\t1\t0.0\t4\t1"
## [154] "107\t1\t0.0\t4\t1"
## [155] "111\t2\t0.0\t4\t2"
## [156] "112\t2\t0.0\t4\t2"
## [157] "113\t2\t0.0\t4\t2"
## [158] "114\t1\t0.0\t4\t1"
## [159] "115\t1\t0.0\t4\t1"
## [160] "118\t1\t0.0\t4\t1"
## [161] "119\t1\t0.0\t4\t1"
## [162] "120\t2\t0.0\t4\t2"
## [163] "121\t2\t0.0\t4\t2"
## [164] "128\t1\t0.0\t4\t1"
## [165] "129\t1\t0.0\t4\t0 1"
## [166] "131\t2\t0.0\t4\t2"
## [167] "143\t1\t0.0\t4\t1"
## [168] "145\t1\t0.0\t4\t1"
## [169] "146\t2\t0.0\t4\t2"
## [170] "147\t1\t0.0\t4\t1"
## [171] "159\t1\t0.0\t4\t0 1"
## [172] "178\t1\t0.0\t4\t1"
## [173] ""
## [174] ""
## [175] "WARNING:"
## [176] " One or more of your adapter sequences may be incomplete."
## [177] " Please see the detailed output above."
##
## [[14]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/105RNA3_S14_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/105RNA3_S14_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/105RNA3_S14_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/105RNA3_S14_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.02 s (272 us/read; 0.22 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 65"
## [9] " Read 1 with adapter: 2 (3.1%)"
## [10] " Read 2 with adapter: 6 (9.2%)"
## [11] "Pairs written (passing filters): 65 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 27,300 bp"
## [14] " Read 1: 12,740 bp"
## [15] " Read 2: 14,560 bp"
## [16] "Total written (filtered): 26,526 bp (97.2%)"
## [17] " Read 1: 12,540 bp"
## [18] " Read 2: 13,986 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 2 times"
## [27] ""
## [28] "No. of allowed errors:"
## [29] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [30] ""
## [31] "Bases preceding removed adapters:"
## [32] " A: 50.0%"
## [33] " C: 0.0%"
## [34] " G: 50.0%"
## [35] " T: 0.0%"
## [36] " none/other: 0.0%"
## [37] ""
## [38] "Overview of removed sequences"
## [39] "length\tcount\texpect\tmax.err\terror counts"
## [40] "61\t1\t0.0\t2\t1"
## [41] "139\t1\t0.0\t2\t1"
## [42] ""
## [43] ""
## [44] "=== Second read: Adapter 3 ==="
## [45] ""
## [46] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [47] ""
## [48] "=== Second read: Adapter 4 ==="
## [49] ""
## [50] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 6 times"
## [51] ""
## [52] "No. of allowed errors:"
## [53] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [54] ""
## [55] "Bases preceding removed adapters:"
## [56] " A: 83.3%"
## [57] " C: 16.7%"
## [58] " G: 0.0%"
## [59] " T: 0.0%"
## [60] " none/other: 0.0%"
## [61] ""
## [62] "Overview of removed sequences"
## [63] "length\tcount\texpect\tmax.err\terror counts"
## [64] "85\t1\t0.0\t4\t1"
## [65] "86\t2\t0.0\t4\t2"
## [66] "89\t1\t0.0\t4\t0 0 1"
## [67] "97\t1\t0.0\t4\t1"
## [68] "131\t1\t0.0\t4\t1"
##
## [[15]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14B1_S15_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14B1_S15_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14B1_S15_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14B1_S15_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 4.41 s (106 us/read; 0.56 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 41,426"
## [9] " Read 1 with adapter: 15 (0.0%)"
## [10] " Read 2 with adapter: 374 (0.9%)"
## [11] "Pairs written (passing filters): 41,425 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 17,398,920 bp"
## [14] " Read 1: 8,119,496 bp"
## [15] " Read 2: 9,279,424 bp"
## [16] "Total written (filtered): 17,375,613 bp (99.9%)"
## [17] " Read 1: 8,118,895 bp"
## [18] " Read 2: 9,256,718 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 11 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t2\t40.5\t0\t2"
## [30] "6\t1\t10.1\t0\t1"
## [31] "7\t1\t2.5\t0\t1"
## [32] "8\t1\t0.6\t0\t1"
## [33] "15\t2\t0.0\t1\t1 1"
## [34] "16\t1\t0.0\t1\t1"
## [35] "23\t1\t0.0\t2\t1"
## [36] "33\t1\t0.0\t3\t1"
## [37] "34\t1\t0.0\t3\t1"
## [38] ""
## [39] ""
## [40] "=== First read: Adapter 2 ==="
## [41] ""
## [42] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 4 times"
## [43] ""
## [44] "No. of allowed errors:"
## [45] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [46] ""
## [47] "Bases preceding removed adapters:"
## [48] " A: 50.0%"
## [49] " C: 0.0%"
## [50] " G: 25.0%"
## [51] " T: 25.0%"
## [52] " none/other: 0.0%"
## [53] ""
## [54] "Overview of removed sequences"
## [55] "length\tcount\texpect\tmax.err\terror counts"
## [56] "5\t1\t40.5\t0\t1"
## [57] "44\t1\t0.0\t2\t1"
## [58] "58\t1\t0.0\t2\t1"
## [59] "131\t1\t0.0\t2\t1"
## [60] ""
## [61] ""
## [62] "=== Second read: Adapter 3 ==="
## [63] ""
## [64] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [65] ""
## [66] "No. of allowed errors:"
## [67] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [68] ""
## [69] "Overview of removed sequences"
## [70] "length\tcount\texpect\tmax.err\terror counts"
## [71] "6\t1\t10.1\t0\t1"
## [72] ""
## [73] ""
## [74] "=== Second read: Adapter 4 ==="
## [75] ""
## [76] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 374 times"
## [77] ""
## [78] "No. of allowed errors:"
## [79] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [80] ""
## [81] "Bases preceding removed adapters:"
## [82] " A: 59.9%"
## [83] " C: 23.8%"
## [84] " G: 15.5%"
## [85] " T: 0.8%"
## [86] " none/other: 0.0%"
## [87] ""
## [88] "Overview of removed sequences"
## [89] "length\tcount\texpect\tmax.err\terror counts"
## [90] "5\t11\t40.5\t0\t11"
## [91] "6\t4\t10.1\t0\t4"
## [92] "7\t3\t2.5\t0\t3"
## [93] "8\t6\t0.6\t0\t6"
## [94] "9\t4\t0.2\t0\t4"
## [95] "10\t2\t0.0\t1\t2"
## [96] "11\t2\t0.0\t1\t2"
## [97] "12\t8\t0.0\t1\t8"
## [98] "13\t1\t0.0\t1\t1"
## [99] "14\t5\t0.0\t1\t5"
## [100] "15\t5\t0.0\t1\t5"
## [101] "16\t10\t0.0\t1\t10"
## [102] "17\t2\t0.0\t1\t2"
## [103] "19\t3\t0.0\t1\t0 3"
## [104] "20\t3\t0.0\t2\t3"
## [105] "21\t2\t0.0\t2\t1 0 1"
## [106] "22\t2\t0.0\t2\t2"
## [107] "23\t1\t0.0\t2\t1"
## [108] "24\t7\t0.0\t2\t6 1"
## [109] "25\t1\t0.0\t2\t1"
## [110] "26\t2\t0.0\t2\t1 1"
## [111] "29\t2\t0.0\t2\t2"
## [112] "30\t4\t0.0\t3\t4"
## [113] "31\t3\t0.0\t3\t2 1"
## [114] "32\t4\t0.0\t3\t3 1"
## [115] "33\t2\t0.0\t3\t0 2"
## [116] "34\t4\t0.0\t3\t3 0 1"
## [117] "35\t6\t0.0\t3\t4 2"
## [118] "36\t2\t0.0\t3\t1 1"
## [119] "37\t1\t0.0\t3\t0 1"
## [120] "38\t9\t0.0\t3\t9"
## [121] "39\t6\t0.0\t3\t4 1 1"
## [122] "40\t5\t0.0\t4\t4 1"
## [123] "41\t4\t0.0\t4\t2 2"
## [124] "42\t7\t0.0\t4\t3 3 1"
## [125] "43\t3\t0.0\t4\t2 1"
## [126] "44\t4\t0.0\t4\t3 1"
## [127] "45\t1\t0.0\t4\t1"
## [128] "46\t4\t0.0\t4\t3 1"
## [129] "47\t4\t0.0\t4\t3 1"
## [130] "48\t4\t0.0\t4\t3 1"
## [131] "50\t2\t0.0\t4\t2"
## [132] "51\t6\t0.0\t4\t5 1"
## [133] "52\t3\t0.0\t4\t3"
## [134] "53\t3\t0.0\t4\t3"
## [135] "54\t2\t0.0\t4\t2"
## [136] "55\t4\t0.0\t4\t2 2"
## [137] "56\t3\t0.0\t4\t2 0 1"
## [138] "57\t5\t0.0\t4\t4 0 1"
## [139] "58\t5\t0.0\t4\t3 2"
## [140] "59\t3\t0.0\t4\t2 0 0 1"
## [141] "60\t1\t0.0\t4\t1"
## [142] "62\t6\t0.0\t4\t4 1 1"
## [143] "63\t6\t0.0\t4\t6"
## [144] "64\t9\t0.0\t4\t9"
## [145] "65\t5\t0.0\t4\t4 1"
## [146] "66\t4\t0.0\t4\t4"
## [147] "69\t2\t0.0\t4\t2"
## [148] "70\t1\t0.0\t4\t1"
## [149] "72\t4\t0.0\t4\t4"
## [150] "73\t2\t0.0\t4\t2"
## [151] "74\t1\t0.0\t4\t1"
## [152] "75\t5\t0.0\t4\t5"
## [153] "76\t5\t0.0\t4\t4 1"
## [154] "77\t2\t0.0\t4\t2"
## [155] "78\t4\t0.0\t4\t3 1"
## [156] "79\t3\t0.0\t4\t3"
## [157] "82\t2\t0.0\t4\t1 1"
## [158] "83\t5\t0.0\t4\t5"
## [159] "84\t7\t0.0\t4\t6 1"
## [160] "85\t7\t0.0\t4\t7"
## [161] "86\t3\t0.0\t4\t2 1"
## [162] "87\t2\t0.0\t4\t2"
## [163] "89\t3\t0.0\t4\t3"
## [164] "90\t3\t0.0\t4\t3"
## [165] "91\t3\t0.0\t4\t3"
## [166] "92\t3\t0.0\t4\t2 1"
## [167] "93\t2\t0.0\t4\t2"
## [168] "94\t2\t0.0\t4\t1 1"
## [169] "95\t2\t0.0\t4\t1 1"
## [170] "96\t2\t0.0\t4\t2"
## [171] "98\t1\t0.0\t4\t1"
## [172] "99\t2\t0.0\t4\t2"
## [173] "100\t2\t0.0\t4\t2"
## [174] "101\t2\t0.0\t4\t2"
## [175] "102\t1\t0.0\t4\t1"
## [176] "103\t2\t0.0\t4\t2"
## [177] "104\t2\t0.0\t4\t2"
## [178] "105\t6\t0.0\t4\t6"
## [179] "106\t1\t0.0\t4\t1"
## [180] "108\t3\t0.0\t4\t3"
## [181] "109\t2\t0.0\t4\t1 1"
## [182] "110\t2\t0.0\t4\t1 1"
## [183] "111\t1\t0.0\t4\t1"
## [184] "112\t2\t0.0\t4\t2"
## [185] "114\t1\t0.0\t4\t1"
## [186] "115\t4\t0.0\t4\t4"
## [187] "117\t2\t0.0\t4\t1 1"
## [188] "118\t2\t0.0\t4\t2"
## [189] "119\t5\t0.0\t4\t4 1"
## [190] "120\t3\t0.0\t4\t1 2"
## [191] "123\t1\t0.0\t4\t1"
## [192] "124\t1\t0.0\t4\t1"
## [193] "125\t2\t0.0\t4\t2"
## [194] "129\t2\t0.0\t4\t2"
## [195] "131\t2\t0.0\t4\t2"
## [196] "132\t2\t0.0\t4\t2"
## [197] "136\t1\t0.0\t4\t1"
## [198] "137\t1\t0.0\t4\t1"
## [199] "138\t2\t0.0\t4\t2"
## [200] "144\t1\t0.0\t4\t1"
## [201] "145\t1\t0.0\t4\t1"
## [202] "147\t1\t0.0\t4\t1"
## [203] "152\t2\t0.0\t4\t2"
## [204] "159\t1\t0.0\t4\t1"
## [205] "163\t1\t0.0\t4\t1"
## [206] "171\t1\t0.0\t4\t1"
## [207] "178\t1\t0.0\t4\t1"
##
## [[16]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14B2_S16_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14B2_S16_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14B2_S16_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14B2_S16_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 3.11 s (106 us/read; 0.57 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 29,473"
## [9] " Read 1 with adapter: 8 (0.0%)"
## [10] " Read 2 with adapter: 273 (0.9%)"
## [11] "Pairs written (passing filters): 29,472 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 12,378,660 bp"
## [14] " Read 1: 5,776,708 bp"
## [15] " Read 2: 6,601,952 bp"
## [16] "Total written (filtered): 12,361,149 bp (99.9%)"
## [17] " Read 1: 5,776,404 bp"
## [18] " Read 2: 6,584,745 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 8 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t3\t28.8\t0\t3"
## [30] "7\t1\t1.8\t0\t1"
## [31] "10\t1\t0.0\t1\t1"
## [32] "19\t1\t0.0\t1\t1"
## [33] "26\t1\t0.0\t2\t1"
## [34] "31\t1\t0.0\t3\t1"
## [35] ""
## [36] ""
## [37] "=== First read: Adapter 2 ==="
## [38] ""
## [39] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 0 times"
## [40] ""
## [41] "=== Second read: Adapter 3 ==="
## [42] ""
## [43] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [44] ""
## [45] "No. of allowed errors:"
## [46] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "5\t1\t28.8\t0\t1"
## [51] ""
## [52] ""
## [53] "=== Second read: Adapter 4 ==="
## [54] ""
## [55] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 273 times"
## [56] ""
## [57] "No. of allowed errors:"
## [58] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [59] ""
## [60] "Bases preceding removed adapters:"
## [61] " A: 55.7%"
## [62] " C: 20.9%"
## [63] " G: 23.4%"
## [64] " T: 0.0%"
## [65] " none/other: 0.0%"
## [66] ""
## [67] "Overview of removed sequences"
## [68] "length\tcount\texpect\tmax.err\terror counts"
## [69] "5\t5\t28.8\t0\t5"
## [70] "6\t3\t7.2\t0\t3"
## [71] "7\t4\t1.8\t0\t4"
## [72] "8\t4\t0.4\t0\t4"
## [73] "9\t4\t0.1\t0\t4"
## [74] "10\t4\t0.0\t1\t4"
## [75] "12\t1\t0.0\t1\t1"
## [76] "13\t3\t0.0\t1\t3"
## [77] "14\t6\t0.0\t1\t6"
## [78] "15\t1\t0.0\t1\t1"
## [79] "16\t9\t0.0\t1\t8 1"
## [80] "17\t4\t0.0\t1\t4"
## [81] "18\t1\t0.0\t1\t1"
## [82] "19\t1\t0.0\t1\t1"
## [83] "20\t2\t0.0\t2\t2"
## [84] "21\t2\t0.0\t2\t2"
## [85] "22\t5\t0.0\t2\t5"
## [86] "23\t5\t0.0\t2\t5"
## [87] "24\t1\t0.0\t2\t1"
## [88] "25\t1\t0.0\t2\t1"
## [89] "27\t3\t0.0\t2\t3"
## [90] "29\t1\t0.0\t2\t1"
## [91] "30\t1\t0.0\t3\t1"
## [92] "32\t3\t0.0\t3\t3"
## [93] "34\t2\t0.0\t3\t2"
## [94] "36\t1\t0.0\t3\t1"
## [95] "38\t1\t0.0\t3\t1"
## [96] "39\t2\t0.0\t3\t1 1"
## [97] "40\t1\t0.0\t4\t1"
## [98] "41\t4\t0.0\t4\t2 2"
## [99] "42\t4\t0.0\t4\t2 1 1"
## [100] "43\t3\t0.0\t4\t3"
## [101] "44\t1\t0.0\t4\t1"
## [102] "46\t2\t0.0\t4\t1 1"
## [103] "47\t1\t0.0\t4\t0 1"
## [104] "48\t3\t0.0\t4\t3"
## [105] "50\t3\t0.0\t4\t2 1"
## [106] "51\t6\t0.0\t4\t3 2 1"
## [107] "52\t3\t0.0\t4\t3"
## [108] "53\t5\t0.0\t4\t4 0 1"
## [109] "54\t4\t0.0\t4\t4"
## [110] "55\t3\t0.0\t4\t3"
## [111] "56\t3\t0.0\t4\t3"
## [112] "57\t3\t0.0\t4\t3"
## [113] "58\t1\t0.0\t4\t1"
## [114] "59\t1\t0.0\t4\t1"
## [115] "60\t1\t0.0\t4\t1"
## [116] "61\t4\t0.0\t4\t4"
## [117] "62\t5\t0.0\t4\t4 1"
## [118] "64\t5\t0.0\t4\t5"
## [119] "65\t5\t0.0\t4\t4 1"
## [120] "66\t4\t0.0\t4\t4"
## [121] "67\t1\t0.0\t4\t1"
## [122] "70\t1\t0.0\t4\t0 1"
## [123] "72\t3\t0.0\t4\t3"
## [124] "73\t5\t0.0\t4\t4 0 0 1"
## [125] "74\t2\t0.0\t4\t2"
## [126] "75\t2\t0.0\t4\t1 1"
## [127] "76\t6\t0.0\t4\t5 1"
## [128] "77\t6\t0.0\t4\t5 0 1"
## [129] "78\t2\t0.0\t4\t2"
## [130] "79\t1\t0.0\t4\t1"
## [131] "80\t3\t0.0\t4\t2 1"
## [132] "81\t2\t0.0\t4\t1 1"
## [133] "83\t3\t0.0\t4\t3"
## [134] "84\t3\t0.0\t4\t3"
## [135] "85\t6\t0.0\t4\t6"
## [136] "86\t6\t0.0\t4\t6"
## [137] "87\t1\t0.0\t4\t1"
## [138] "89\t3\t0.0\t4\t3"
## [139] "90\t2\t0.0\t4\t2"
## [140] "91\t2\t0.0\t4\t1 1"
## [141] "92\t2\t0.0\t4\t1 0 0 1"
## [142] "93\t1\t0.0\t4\t0 1"
## [143] "94\t5\t0.0\t4\t5"
## [144] "95\t2\t0.0\t4\t2"
## [145] "96\t3\t0.0\t4\t2 1"
## [146] "97\t1\t0.0\t4\t1"
## [147] "98\t4\t0.0\t4\t3 1"
## [148] "101\t2\t0.0\t4\t2"
## [149] "102\t2\t0.0\t4\t2"
## [150] "103\t1\t0.0\t4\t1"
## [151] "105\t1\t0.0\t4\t1"
## [152] "109\t1\t0.0\t4\t1"
## [153] "111\t2\t0.0\t4\t1 1"
## [154] "112\t1\t0.0\t4\t1"
## [155] "113\t1\t0.0\t4\t1"
## [156] "115\t1\t0.0\t4\t1"
## [157] "116\t1\t0.0\t4\t0 1"
## [158] "118\t1\t0.0\t4\t1"
## [159] "119\t3\t0.0\t4\t2 1"
## [160] "120\t3\t0.0\t4\t3"
## [161] "121\t1\t0.0\t4\t1"
## [162] "125\t1\t0.0\t4\t1"
## [163] "127\t1\t0.0\t4\t1"
## [164] "130\t1\t0.0\t4\t1"
## [165] "131\t1\t0.0\t4\t1"
## [166] "140\t1\t0.0\t4\t1"
## [167] "142\t1\t0.0\t4\t1"
## [168] "143\t2\t0.0\t4\t2"
## [169] "148\t1\t0.0\t4\t1"
## [170] "149\t1\t0.0\t4\t1"
## [171] "152\t1\t0.0\t4\t0 1"
## [172] "153\t1\t0.0\t4\t0 1"
## [173] "157\t1\t0.0\t4\t1"
## [174] "158\t3\t0.0\t4\t3"
## [175] "160\t1\t0.0\t4\t1"
## [176] "164\t1\t0.0\t4\t1"
## [177] "178\t1\t0.0\t4\t1"
##
## [[17]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14B3_S17_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14B3_S17_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14B3_S17_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14B3_S17_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 3.01 s (104 us/read; 0.58 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 29,025"
## [9] " Read 1 with adapter: 12 (0.0%)"
## [10] " Read 2 with adapter: 278 (1.0%)"
## [11] "Pairs written (passing filters): 29,025 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 12,190,500 bp"
## [14] " Read 1: 5,688,900 bp"
## [15] " Read 2: 6,501,600 bp"
## [16] "Total written (filtered): 12,171,800 bp (99.8%)"
## [17] " Read 1: 5,688,370 bp"
## [18] " Read 2: 6,483,430 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 9 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "6\t1\t7.1\t0\t1"
## [30] "7\t1\t1.8\t0\t1"
## [31] "12\t1\t0.0\t1\t1"
## [32] "16\t1\t0.0\t1\t1"
## [33] "17\t1\t0.0\t1\t1"
## [34] "18\t1\t0.0\t1\t0 1"
## [35] "20\t1\t0.0\t2\t1"
## [36] "22\t1\t0.0\t2\t1"
## [37] "23\t1\t0.0\t2\t1"
## [38] ""
## [39] ""
## [40] "=== First read: Adapter 2 ==="
## [41] ""
## [42] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 3 times"
## [43] ""
## [44] "No. of allowed errors:"
## [45] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [46] ""
## [47] "Bases preceding removed adapters:"
## [48] " A: 33.3%"
## [49] " C: 0.0%"
## [50] " G: 33.3%"
## [51] " T: 33.3%"
## [52] " none/other: 0.0%"
## [53] ""
## [54] "Overview of removed sequences"
## [55] "length\tcount\texpect\tmax.err\terror counts"
## [56] "112\t1\t0.0\t2\t1"
## [57] "131\t1\t0.0\t2\t1"
## [58] "146\t1\t0.0\t2\t1"
## [59] ""
## [60] ""
## [61] "=== Second read: Adapter 3 ==="
## [62] ""
## [63] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [64] ""
## [65] "=== Second read: Adapter 4 ==="
## [66] ""
## [67] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 278 times"
## [68] ""
## [69] "No. of allowed errors:"
## [70] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [71] ""
## [72] "Bases preceding removed adapters:"
## [73] " A: 58.3%"
## [74] " C: 21.9%"
## [75] " G: 19.1%"
## [76] " T: 0.7%"
## [77] " none/other: 0.0%"
## [78] ""
## [79] "Overview of removed sequences"
## [80] "length\tcount\texpect\tmax.err\terror counts"
## [81] "5\t9\t28.3\t0\t9"
## [82] "6\t3\t7.1\t0\t3"
## [83] "7\t2\t1.8\t0\t2"
## [84] "8\t4\t0.4\t0\t4"
## [85] "9\t3\t0.1\t0\t3"
## [86] "10\t3\t0.0\t1\t3"
## [87] "11\t1\t0.0\t1\t0 1"
## [88] "12\t5\t0.0\t1\t4 1"
## [89] "14\t14\t0.0\t1\t14"
## [90] "15\t4\t0.0\t1\t4"
## [91] "16\t7\t0.0\t1\t5 2"
## [92] "17\t2\t0.0\t1\t2"
## [93] "18\t3\t0.0\t1\t2 1"
## [94] "19\t2\t0.0\t1\t2"
## [95] "20\t1\t0.0\t2\t1"
## [96] "21\t3\t0.0\t2\t3"
## [97] "22\t3\t0.0\t2\t3"
## [98] "23\t1\t0.0\t2\t0 1"
## [99] "24\t1\t0.0\t2\t1"
## [100] "25\t1\t0.0\t2\t0 1"
## [101] "26\t1\t0.0\t2\t1"
## [102] "27\t2\t0.0\t2\t2"
## [103] "28\t1\t0.0\t2\t1"
## [104] "31\t1\t0.0\t3\t0 1"
## [105] "32\t2\t0.0\t3\t2"
## [106] "33\t1\t0.0\t3\t1"
## [107] "34\t3\t0.0\t3\t3"
## [108] "36\t2\t0.0\t3\t2"
## [109] "38\t2\t0.0\t3\t1 1"
## [110] "39\t3\t0.0\t3\t3"
## [111] "41\t3\t0.0\t4\t3"
## [112] "43\t2\t0.0\t4\t0 2"
## [113] "44\t3\t0.0\t4\t3"
## [114] "45\t3\t0.0\t4\t2 1"
## [115] "50\t2\t0.0\t4\t2"
## [116] "51\t1\t0.0\t4\t1"
## [117] "52\t5\t0.0\t4\t3 1 1"
## [118] "53\t4\t0.0\t4\t3 1"
## [119] "55\t2\t0.0\t4\t2"
## [120] "56\t7\t0.0\t4\t7"
## [121] "57\t2\t0.0\t4\t2"
## [122] "58\t2\t0.0\t4\t2"
## [123] "59\t4\t0.0\t4\t3 1"
## [124] "60\t3\t0.0\t4\t3"
## [125] "61\t1\t0.0\t4\t1"
## [126] "62\t2\t0.0\t4\t2"
## [127] "63\t6\t0.0\t4\t4 2"
## [128] "64\t4\t0.0\t4\t1 2 0 1"
## [129] "65\t4\t0.0\t4\t4"
## [130] "66\t3\t0.0\t4\t3"
## [131] "67\t2\t0.0\t4\t2"
## [132] "69\t3\t0.0\t4\t1 2"
## [133] "70\t1\t0.0\t4\t0 1"
## [134] "71\t1\t0.0\t4\t1"
## [135] "72\t1\t0.0\t4\t1"
## [136] "73\t3\t0.0\t4\t1 2"
## [137] "74\t2\t0.0\t4\t2"
## [138] "75\t1\t0.0\t4\t1"
## [139] "77\t3\t0.0\t4\t2 1"
## [140] "79\t4\t0.0\t4\t4"
## [141] "80\t1\t0.0\t4\t1"
## [142] "81\t3\t0.0\t4\t2 1"
## [143] "82\t1\t0.0\t4\t1"
## [144] "83\t3\t0.0\t4\t2 0 0 1"
## [145] "84\t2\t0.0\t4\t2"
## [146] "85\t8\t0.0\t4\t7 0 0 1"
## [147] "86\t1\t0.0\t4\t1"
## [148] "87\t1\t0.0\t4\t1"
## [149] "88\t1\t0.0\t4\t1"
## [150] "90\t1\t0.0\t4\t0 1"
## [151] "91\t2\t0.0\t4\t2"
## [152] "93\t1\t0.0\t4\t1"
## [153] "94\t4\t0.0\t4\t2 2"
## [154] "98\t4\t0.0\t4\t4"
## [155] "99\t1\t0.0\t4\t1"
## [156] "100\t2\t0.0\t4\t2"
## [157] "101\t3\t0.0\t4\t3"
## [158] "102\t4\t0.0\t4\t4"
## [159] "103\t2\t0.0\t4\t2"
## [160] "105\t8\t0.0\t4\t8"
## [161] "107\t2\t0.0\t4\t2"
## [162] "109\t1\t0.0\t4\t1"
## [163] "110\t1\t0.0\t4\t1"
## [164] "112\t1\t0.0\t4\t1"
## [165] "113\t1\t0.0\t4\t1"
## [166] "115\t3\t0.0\t4\t2 1"
## [167] "117\t3\t0.0\t4\t3"
## [168] "118\t2\t0.0\t4\t2"
## [169] "119\t4\t0.0\t4\t4"
## [170] "120\t1\t0.0\t4\t1"
## [171] "121\t3\t0.0\t4\t3"
## [172] "124\t2\t0.0\t4\t2"
## [173] "125\t1\t0.0\t4\t1"
## [174] "126\t2\t0.0\t4\t2"
## [175] "127\t2\t0.0\t4\t2"
## [176] "128\t2\t0.0\t4\t2"
## [177] "130\t1\t0.0\t4\t1"
## [178] "131\t1\t0.0\t4\t1"
## [179] "133\t1\t0.0\t4\t1"
## [180] "136\t2\t0.0\t4\t2"
## [181] "138\t1\t0.0\t4\t0 0 1"
## [182] "140\t3\t0.0\t4\t3"
## [183] "141\t1\t0.0\t4\t1"
## [184] "142\t1\t0.0\t4\t1"
## [185] "144\t1\t0.0\t4\t1"
## [186] "145\t1\t0.0\t4\t1"
## [187] "147\t1\t0.0\t4\t1"
## [188] "151\t1\t0.0\t4\t0 1"
## [189] "156\t1\t0.0\t4\t1"
## [190] "159\t1\t0.0\t4\t1"
## [191] "162\t1\t0.0\t4\t1"
## [192] "170\t1\t0.0\t4\t1"
## [193] "171\t1\t0.0\t4\t1"
##
## [[18]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14B4_S18_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14B4_S18_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14B4_S18_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14B4_S18_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.67 s (107 us/read; 0.56 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 15,610"
## [9] " Read 1 with adapter: 11 (0.1%)"
## [10] " Read 2 with adapter: 168 (1.1%)"
## [11] "Pairs written (passing filters): 15,609 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 6,556,200 bp"
## [14] " Read 1: 3,059,560 bp"
## [15] " Read 2: 3,496,640 bp"
## [16] "Total written (filtered): 6,544,266 bp (99.8%)"
## [17] " Read 1: 3,058,822 bp"
## [18] " Read 2: 3,485,444 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 5 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t15.2\t0\t1"
## [30] "6\t2\t3.8\t0\t2"
## [31] "11\t1\t0.0\t1\t1"
## [32] "16\t1\t0.0\t1\t1"
## [33] ""
## [34] ""
## [35] "=== First read: Adapter 2 ==="
## [36] ""
## [37] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 6 times"
## [38] ""
## [39] "No. of allowed errors:"
## [40] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [41] ""
## [42] "Bases preceding removed adapters:"
## [43] " A: 0.0%"
## [44] " C: 0.0%"
## [45] " G: 100.0%"
## [46] " T: 0.0%"
## [47] " none/other: 0.0%"
## [48] ""
## [49] "Overview of removed sequences"
## [50] "length\tcount\texpect\tmax.err\terror counts"
## [51] "19\t1\t0.0\t1\t1"
## [52] "90\t4\t0.0\t2\t4"
## [53] "119\t1\t0.0\t2\t1"
## [54] ""
## [55] ""
## [56] "=== Second read: Adapter 3 ==="
## [57] ""
## [58] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [59] ""
## [60] "No. of allowed errors:"
## [61] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [62] ""
## [63] "Overview of removed sequences"
## [64] "length\tcount\texpect\tmax.err\terror counts"
## [65] "55\t1\t0.0\t2\t1"
## [66] ""
## [67] ""
## [68] "=== Second read: Adapter 4 ==="
## [69] ""
## [70] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 167 times"
## [71] ""
## [72] "No. of allowed errors:"
## [73] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [74] ""
## [75] "Bases preceding removed adapters:"
## [76] " A: 63.5%"
## [77] " C: 13.8%"
## [78] " G: 20.4%"
## [79] " T: 2.4%"
## [80] " none/other: 0.0%"
## [81] ""
## [82] "Overview of removed sequences"
## [83] "length\tcount\texpect\tmax.err\terror counts"
## [84] "5\t3\t15.2\t0\t3"
## [85] "6\t1\t3.8\t0\t1"
## [86] "7\t2\t1.0\t0\t2"
## [87] "8\t6\t0.2\t0\t6"
## [88] "9\t3\t0.1\t0\t3"
## [89] "12\t2\t0.0\t1\t1 1"
## [90] "14\t4\t0.0\t1\t4"
## [91] "15\t2\t0.0\t1\t2"
## [92] "16\t2\t0.0\t1\t2"
## [93] "18\t1\t0.0\t1\t1"
## [94] "19\t2\t0.0\t1\t2"
## [95] "20\t2\t0.0\t2\t2"
## [96] "22\t2\t0.0\t2\t2"
## [97] "23\t2\t0.0\t2\t2"
## [98] "24\t2\t0.0\t2\t1 1"
## [99] "25\t2\t0.0\t2\t1 1"
## [100] "26\t2\t0.0\t2\t1 1"
## [101] "27\t2\t0.0\t2\t1 1"
## [102] "28\t1\t0.0\t2\t0 0 1"
## [103] "29\t1\t0.0\t2\t1"
## [104] "30\t1\t0.0\t3\t1"
## [105] "31\t1\t0.0\t3\t0 1"
## [106] "32\t4\t0.0\t3\t4"
## [107] "33\t1\t0.0\t3\t1"
## [108] "34\t1\t0.0\t3\t1"
## [109] "35\t2\t0.0\t3\t2"
## [110] "36\t1\t0.0\t3\t1"
## [111] "39\t1\t0.0\t3\t1"
## [112] "42\t1\t0.0\t4\t1"
## [113] "43\t1\t0.0\t4\t1"
## [114] "44\t4\t0.0\t4\t2 2"
## [115] "45\t3\t0.0\t4\t3"
## [116] "46\t1\t0.0\t4\t1"
## [117] "47\t2\t0.0\t4\t1 1"
## [118] "49\t2\t0.0\t4\t2"
## [119] "51\t1\t0.0\t4\t1"
## [120] "52\t4\t0.0\t4\t4"
## [121] "54\t1\t0.0\t4\t1"
## [122] "57\t2\t0.0\t4\t2"
## [123] "58\t1\t0.0\t4\t1"
## [124] "59\t2\t0.0\t4\t1 0 0 0 1"
## [125] "60\t1\t0.0\t4\t1"
## [126] "63\t2\t0.0\t4\t2"
## [127] "64\t4\t0.0\t4\t3 1"
## [128] "65\t5\t0.0\t4\t5"
## [129] "66\t1\t0.0\t4\t1"
## [130] "67\t1\t0.0\t4\t1"
## [131] "69\t1\t0.0\t4\t0 0 0 0 1"
## [132] "72\t2\t0.0\t4\t2"
## [133] "73\t2\t0.0\t4\t2"
## [134] "74\t1\t0.0\t4\t1"
## [135] "75\t1\t0.0\t4\t1"
## [136] "77\t2\t0.0\t4\t2"
## [137] "79\t2\t0.0\t4\t1 1"
## [138] "81\t1\t0.0\t4\t1"
## [139] "82\t1\t0.0\t4\t1"
## [140] "84\t3\t0.0\t4\t3"
## [141] "85\t4\t0.0\t4\t3 0 1"
## [142] "86\t2\t0.0\t4\t2"
## [143] "92\t1\t0.0\t4\t1"
## [144] "93\t2\t0.0\t4\t2"
## [145] "94\t1\t0.0\t4\t1"
## [146] "95\t1\t0.0\t4\t1"
## [147] "96\t1\t0.0\t4\t1"
## [148] "97\t1\t0.0\t4\t1"
## [149] "99\t2\t0.0\t4\t2"
## [150] "105\t2\t0.0\t4\t1 1"
## [151] "106\t1\t0.0\t4\t1"
## [152] "108\t1\t0.0\t4\t1"
## [153] "109\t1\t0.0\t4\t1"
## [154] "111\t2\t0.0\t4\t2"
## [155] "112\t1\t0.0\t4\t1"
## [156] "114\t1\t0.0\t4\t1"
## [157] "115\t1\t0.0\t4\t1"
## [158] "116\t1\t0.0\t4\t1"
## [159] "117\t1\t0.0\t4\t1"
## [160] "118\t5\t0.0\t4\t5"
## [161] "119\t1\t0.0\t4\t1"
## [162] "120\t1\t0.0\t4\t1"
## [163] "123\t1\t0.0\t4\t1"
## [164] "124\t2\t0.0\t4\t2"
## [165] "125\t1\t0.0\t4\t1"
## [166] "126\t1\t0.0\t4\t1"
## [167] "127\t1\t0.0\t4\t1"
## [168] "128\t1\t0.0\t4\t1"
## [169] "129\t1\t0.0\t4\t0 1"
## [170] "135\t1\t0.0\t4\t1"
## [171] "138\t1\t0.0\t4\t1"
## [172] "140\t3\t0.0\t4\t2 1"
## [173] "146\t1\t0.0\t4\t1"
## [174] "147\t4\t0.0\t4\t3 1"
## [175] "151\t1\t0.0\t4\t1"
## [176] "160\t1\t0.0\t4\t1"
## [177] "173\t1\t0.0\t4\t1"
## [178] "184\t1\t0.0\t4\t1"
##
## [[19]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14BRNA1_S19_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14BRNA1_S19_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14BRNA1_S19_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14BRNA1_S19_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.88 s (112 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 7,870"
## [9] " Read 1 with adapter: 206 (2.6%)"
## [10] " Read 2 with adapter: 711 (9.0%)"
## [11] "Pairs written (passing filters): 7,867 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,305,400 bp"
## [14] " Read 1: 1,542,520 bp"
## [15] " Read 2: 1,762,880 bp"
## [16] "Total written (filtered): 3,233,958 bp (97.8%)"
## [17] " Read 1: 1,528,627 bp"
## [18] " Read 2: 1,705,331 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 4 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "12\t1\t0.0\t1\t1"
## [30] "33\t2\t0.0\t3\t0 1 1"
## [31] "35\t1\t0.0\t3\t0 0 1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 202 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 74.3%"
## [43] " C: 2.5%"
## [44] " G: 17.8%"
## [45] " T: 5.4%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "9\t1\t0.0\t0\t1"
## [51] "11\t1\t0.0\t1\t1"
## [52] "15\t1\t0.0\t1\t1"
## [53] "20\t1\t0.0\t2\t1"
## [54] "28\t1\t0.0\t2\t1"
## [55] "36\t4\t0.0\t2\t4"
## [56] "54\t5\t0.0\t2\t3 2"
## [57] "55\t2\t0.0\t2\t2"
## [58] "56\t1\t0.0\t2\t1"
## [59] "59\t2\t0.0\t2\t2"
## [60] "60\t4\t0.0\t2\t4"
## [61] "61\t124\t0.0\t2\t123 1"
## [62] "62\t6\t0.0\t2\t6"
## [63] "63\t2\t0.0\t2\t1 1"
## [64] "64\t1\t0.0\t2\t1"
## [65] "67\t1\t0.0\t2\t1"
## [66] "70\t1\t0.0\t2\t1"
## [67] "74\t3\t0.0\t2\t3"
## [68] "78\t2\t0.0\t2\t1 1"
## [69] "81\t3\t0.0\t2\t3"
## [70] "82\t7\t0.0\t2\t7"
## [71] "84\t1\t0.0\t2\t1"
## [72] "90\t20\t0.0\t2\t20"
## [73] "92\t1\t0.0\t2\t1"
## [74] "96\t4\t0.0\t2\t4"
## [75] "111\t1\t0.0\t2\t1"
## [76] "119\t1\t0.0\t2\t1"
## [77] "123\t1\t0.0\t2\t1"
## [78] ""
## [79] ""
## [80] "=== Second read: Adapter 3 ==="
## [81] ""
## [82] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [83] ""
## [84] "No. of allowed errors:"
## [85] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [86] ""
## [87] "Overview of removed sequences"
## [88] "length\tcount\texpect\tmax.err\terror counts"
## [89] "5\t1\t7.7\t0\t1"
## [90] ""
## [91] ""
## [92] "=== Second read: Adapter 4 ==="
## [93] ""
## [94] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 711 times"
## [95] ""
## [96] "No. of allowed errors:"
## [97] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [98] ""
## [99] "Bases preceding removed adapters:"
## [100] " A: 69.3%"
## [101] " C: 12.4%"
## [102] " G: 18.0%"
## [103] " T: 0.3%"
## [104] " none/other: 0.0%"
## [105] ""
## [106] "Overview of removed sequences"
## [107] "length\tcount\texpect\tmax.err\terror counts"
## [108] "5\t2\t7.7\t0\t2"
## [109] "6\t5\t1.9\t0\t5"
## [110] "7\t1\t0.5\t0\t1"
## [111] "8\t7\t0.1\t0\t7"
## [112] "11\t1\t0.0\t1\t1"
## [113] "12\t1\t0.0\t1\t1"
## [114] "13\t2\t0.0\t1\t1 1"
## [115] "14\t9\t0.0\t1\t5 4"
## [116] "15\t7\t0.0\t1\t6 1"
## [117] "16\t10\t0.0\t1\t9 1"
## [118] "17\t4\t0.0\t1\t3 1"
## [119] "18\t1\t0.0\t1\t1"
## [120] "19\t1\t0.0\t1\t1"
## [121] "20\t4\t0.0\t2\t1 2 1"
## [122] "21\t1\t0.0\t2\t0 1"
## [123] "22\t3\t0.0\t2\t2 0 1"
## [124] "23\t2\t0.0\t2\t1 1"
## [125] "24\t4\t0.0\t2\t3 1"
## [126] "25\t3\t0.0\t2\t1 1 1"
## [127] "26\t4\t0.0\t2\t4"
## [128] "27\t3\t0.0\t2\t1 2"
## [129] "28\t2\t0.0\t2\t1 1"
## [130] "30\t4\t0.0\t3\t3 1"
## [131] "31\t6\t0.0\t3\t2 2 1 1"
## [132] "32\t2\t0.0\t3\t1 1"
## [133] "33\t3\t0.0\t3\t2 0 1"
## [134] "34\t5\t0.0\t3\t3 1 0 1"
## [135] "35\t7\t0.0\t3\t5 2"
## [136] "37\t1\t0.0\t3\t1"
## [137] "38\t2\t0.0\t3\t0 2"
## [138] "39\t5\t0.0\t3\t1 2 1 1"
## [139] "40\t1\t0.0\t4\t1"
## [140] "41\t5\t0.0\t4\t3 1 1"
## [141] "42\t3\t0.0\t4\t2 1"
## [142] "43\t5\t0.0\t4\t3 1 1"
## [143] "44\t1\t0.0\t4\t1"
## [144] "45\t6\t0.0\t4\t3 3"
## [145] "46\t6\t0.0\t4\t3 3"
## [146] "47\t3\t0.0\t4\t0 1 1 1"
## [147] "48\t7\t0.0\t4\t7"
## [148] "49\t3\t0.0\t4\t2 0 1"
## [149] "50\t3\t0.0\t4\t2 1"
## [150] "51\t4\t0.0\t4\t2 0 2"
## [151] "52\t8\t0.0\t4\t3 2 2 1"
## [152] "53\t2\t0.0\t4\t1 1"
## [153] "54\t1\t0.0\t4\t1"
## [154] "55\t2\t0.0\t4\t1 1"
## [155] "56\t7\t0.0\t4\t3 2 0 1 1"
## [156] "57\t1\t0.0\t4\t1"
## [157] "58\t7\t0.0\t4\t7"
## [158] "59\t6\t0.0\t4\t5 1"
## [159] "60\t2\t0.0\t4\t1 0 0 0 1"
## [160] "61\t4\t0.0\t4\t4"
## [161] "62\t3\t0.0\t4\t2 1"
## [162] "63\t6\t0.0\t4\t3 3"
## [163] "64\t14\t0.0\t4\t10 2 2"
## [164] "65\t5\t0.0\t4\t3 2"
## [165] "66\t3\t0.0\t4\t2 1"
## [166] "67\t3\t0.0\t4\t3"
## [167] "68\t2\t0.0\t4\t1 1"
## [168] "70\t2\t0.0\t4\t1 1"
## [169] "71\t4\t0.0\t4\t3 1"
## [170] "72\t4\t0.0\t4\t3 1"
## [171] "73\t3\t0.0\t4\t2 1"
## [172] "74\t5\t0.0\t4\t3 2"
## [173] "75\t10\t0.0\t4\t5 4 0 1"
## [174] "76\t6\t0.0\t4\t2 4"
## [175] "77\t6\t0.0\t4\t5 1"
## [176] "78\t3\t0.0\t4\t2 1"
## [177] "79\t8\t0.0\t4\t6 2"
## [178] "80\t2\t0.0\t4\t1 1"
## [179] "81\t5\t0.0\t4\t3 1 0 1"
## [180] "82\t8\t0.0\t4\t3 4 1"
## [181] "83\t10\t0.0\t4\t6 3 0 0 1"
## [182] "84\t13\t0.0\t4\t10 3"
## [183] "85\t10\t0.0\t4\t8 2"
## [184] "86\t14\t0.0\t4\t9 5"
## [185] "87\t4\t0.0\t4\t1 2 1"
## [186] "88\t8\t0.0\t4\t2 5 0 0 1"
## [187] "89\t133\t0.0\t4\t8 100 18 4 3"
## [188] "90\t3\t0.0\t4\t3"
## [189] "91\t4\t0.0\t4\t3 1"
## [190] "92\t6\t0.0\t4\t4 1 0 0 1"
## [191] "93\t5\t0.0\t4\t4 1"
## [192] "94\t12\t0.0\t4\t8 2 2"
## [193] "95\t3\t0.0\t4\t3"
## [194] "96\t1\t0.0\t4\t1"
## [195] "97\t2\t0.0\t4\t2"
## [196] "98\t2\t0.0\t4\t1 1"
## [197] "99\t2\t0.0\t4\t2"
## [198] "101\t1\t0.0\t4\t0 1"
## [199] "102\t6\t0.0\t4\t6"
## [200] "103\t2\t0.0\t4\t2"
## [201] "104\t1\t0.0\t4\t1"
## [202] "105\t1\t0.0\t4\t0 1"
## [203] "106\t6\t0.0\t4\t4 2"
## [204] "107\t3\t0.0\t4\t1 2"
## [205] "108\t3\t0.0\t4\t2 1"
## [206] "109\t7\t0.0\t4\t3 4"
## [207] "110\t13\t0.0\t4\t4 9"
## [208] "111\t1\t0.0\t4\t0 1"
## [209] "112\t5\t0.0\t4\t2 3"
## [210] "113\t5\t0.0\t4\t5"
## [211] "115\t1\t0.0\t4\t1"
## [212] "116\t4\t0.0\t4\t4"
## [213] "117\t5\t0.0\t4\t4 1"
## [214] "118\t24\t0.0\t4\t8 13 2 0 1"
## [215] "119\t4\t0.0\t4\t3 0 1"
## [216] "120\t5\t0.0\t4\t3 2"
## [217] "121\t3\t0.0\t4\t3"
## [218] "122\t3\t0.0\t4\t3"
## [219] "123\t1\t0.0\t4\t0 1"
## [220] "124\t5\t0.0\t4\t4 1"
## [221] "125\t2\t0.0\t4\t1 1"
## [222] "126\t2\t0.0\t4\t1 1"
## [223] "127\t1\t0.0\t4\t1"
## [224] "128\t5\t0.0\t4\t5"
## [225] "130\t2\t0.0\t4\t1 1"
## [226] "131\t1\t0.0\t4\t1"
## [227] "132\t1\t0.0\t4\t1"
## [228] "133\t1\t0.0\t4\t1"
## [229] "134\t1\t0.0\t4\t1"
## [230] "136\t2\t0.0\t4\t2"
## [231] "137\t1\t0.0\t4\t1"
## [232] "139\t6\t0.0\t4\t5 1"
## [233] "140\t4\t0.0\t4\t4"
## [234] "141\t5\t0.0\t4\t4 0 1"
## [235] "142\t1\t0.0\t4\t1"
## [236] "145\t1\t0.0\t4\t0 1"
## [237] "146\t1\t0.0\t4\t1"
## [238] "147\t4\t0.0\t4\t2 2"
## [239] "148\t1\t0.0\t4\t1"
## [240] "149\t1\t0.0\t4\t1"
## [241] "150\t1\t0.0\t4\t1"
## [242] "151\t2\t0.0\t4\t0 2"
## [243] "153\t1\t0.0\t4\t0 0 1"
## [244] "154\t1\t0.0\t4\t1"
## [245] "155\t1\t0.0\t4\t1"
## [246] "158\t1\t0.0\t4\t1"
## [247] "159\t1\t0.0\t4\t0 1"
## [248] "160\t2\t0.0\t4\t1 1"
## [249] "162\t2\t0.0\t4\t1 1"
## [250] "166\t2\t0.0\t4\t2"
## [251] "167\t2\t0.0\t4\t1 1"
## [252] "168\t2\t0.0\t4\t1 1"
## [253] "171\t1\t0.0\t4\t1"
## [254] "172\t2\t0.0\t4\t2"
## [255] "173\t2\t0.0\t4\t2"
## [256] "175\t2\t0.0\t4\t2"
## [257] "178\t1\t0.0\t4\t1"
##
## [[20]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14BRNA2_S20_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14BRNA2_S20_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14BRNA2_S20_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14BRNA2_S20_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.91 s (110 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 8,222"
## [9] " Read 1 with adapter: 260 (3.2%)"
## [10] " Read 2 with adapter: 1,543 (18.8%)"
## [11] "Pairs written (passing filters): 8,219 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,453,240 bp"
## [14] " Read 1: 1,611,512 bp"
## [15] " Read 2: 1,841,728 bp"
## [16] "Total written (filtered): 3,312,619 bp (95.9%)"
## [17] " Read 1: 1,594,065 bp"
## [18] " Read 2: 1,718,554 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 12 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "6\t2\t2.0\t0\t2"
## [30] "17\t5\t0.0\t1\t4 1"
## [31] "18\t1\t0.0\t1\t1"
## [32] "28\t1\t0.0\t2\t1"
## [33] "31\t1\t0.0\t3\t1"
## [34] "33\t1\t0.0\t3\t0 0 1"
## [35] "35\t1\t0.0\t3\t0 1"
## [36] ""
## [37] ""
## [38] "=== First read: Adapter 2 ==="
## [39] ""
## [40] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 249 times"
## [41] ""
## [42] "No. of allowed errors:"
## [43] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [44] ""
## [45] "Bases preceding removed adapters:"
## [46] " A: 58.6%"
## [47] " C: 2.4%"
## [48] " G: 32.1%"
## [49] " T: 6.8%"
## [50] " none/other: 0.0%"
## [51] ""
## [52] "Overview of removed sequences"
## [53] "length\tcount\texpect\tmax.err\terror counts"
## [54] "5\t1\t8.0\t0\t1"
## [55] "6\t1\t2.0\t0\t1"
## [56] "8\t3\t0.1\t0\t3"
## [57] "10\t1\t0.0\t1\t1"
## [58] "11\t1\t0.0\t1\t1"
## [59] "12\t1\t0.0\t1\t1"
## [60] "13\t1\t0.0\t1\t1"
## [61] "16\t1\t0.0\t1\t1"
## [62] "19\t1\t0.0\t1\t1"
## [63] "28\t1\t0.0\t2\t1"
## [64] "29\t1\t0.0\t2\t1"
## [65] "30\t1\t0.0\t2\t1"
## [66] "36\t4\t0.0\t2\t4"
## [67] "37\t1\t0.0\t2\t1"
## [68] "39\t1\t0.0\t2\t1"
## [69] "42\t2\t0.0\t2\t2"
## [70] "43\t2\t0.0\t2\t2"
## [71] "45\t1\t0.0\t2\t1"
## [72] "47\t1\t0.0\t2\t1"
## [73] "52\t1\t0.0\t2\t1"
## [74] "54\t3\t0.0\t2\t3"
## [75] "55\t2\t0.0\t2\t2"
## [76] "57\t1\t0.0\t2\t1"
## [77] "58\t1\t0.0\t2\t1"
## [78] "59\t2\t0.0\t2\t2"
## [79] "60\t2\t0.0\t2\t1 1"
## [80] "61\t108\t0.0\t2\t104 4"
## [81] "62\t9\t0.0\t2\t9"
## [82] "71\t1\t0.0\t2\t1"
## [83] "73\t1\t0.0\t2\t1"
## [84] "74\t12\t0.0\t2\t12"
## [85] "75\t1\t0.0\t2\t1"
## [86] "77\t2\t0.0\t2\t2"
## [87] "80\t2\t0.0\t2\t2"
## [88] "81\t5\t0.0\t2\t5"
## [89] "82\t11\t0.0\t2\t10 1"
## [90] "86\t2\t0.0\t2\t2"
## [91] "88\t1\t0.0\t2\t1"
## [92] "90\t38\t0.0\t2\t37 1"
## [93] "91\t3\t0.0\t2\t3"
## [94] "92\t2\t0.0\t2\t2"
## [95] "95\t1\t0.0\t2\t1"
## [96] "96\t2\t0.0\t2\t2"
## [97] "104\t1\t0.0\t2\t1"
## [98] "105\t1\t0.0\t2\t1"
## [99] "108\t1\t0.0\t2\t1"
## [100] "111\t1\t0.0\t2\t1"
## [101] "123\t2\t0.0\t2\t2"
## [102] "140\t1\t0.0\t2\t1"
## [103] "143\t1\t0.0\t2\t1"
## [104] "147\t1\t0.0\t2\t1"
## [105] "152\t1\t0.0\t2\t1"
## [106] ""
## [107] ""
## [108] "=== Second read: Adapter 3 ==="
## [109] ""
## [110] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 17 times"
## [111] ""
## [112] "No. of allowed errors:"
## [113] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [114] ""
## [115] "Overview of removed sequences"
## [116] "length\tcount\texpect\tmax.err\terror counts"
## [117] "5\t2\t8.0\t0\t2"
## [118] "6\t1\t2.0\t0\t1"
## [119] "19\t1\t0.0\t1\t1"
## [120] "29\t1\t0.0\t2\t1"
## [121] "98\t1\t0.0\t2\t1"
## [122] "123\t1\t0.0\t2\t1"
## [123] "125\t10\t0.0\t2\t9 1"
## [124] ""
## [125] ""
## [126] "=== Second read: Adapter 4 ==="
## [127] ""
## [128] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 1528 times"
## [129] ""
## [130] "No. of allowed errors:"
## [131] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [132] ""
## [133] "Bases preceding removed adapters:"
## [134] " A: 43.4%"
## [135] " C: 8.6%"
## [136] " G: 47.9%"
## [137] " T: 0.1%"
## [138] " none/other: 0.0%"
## [139] ""
## [140] "Overview of removed sequences"
## [141] "length\tcount\texpect\tmax.err\terror counts"
## [142] "5\t3\t8.0\t0\t3"
## [143] "6\t3\t2.0\t0\t3"
## [144] "7\t7\t0.5\t0\t7"
## [145] "8\t11\t0.1\t0\t11"
## [146] "9\t3\t0.0\t0\t3"
## [147] "10\t4\t0.0\t1\t4"
## [148] "12\t8\t0.0\t1\t7 1"
## [149] "13\t6\t0.0\t1\t4 2"
## [150] "14\t12\t0.0\t1\t11 1"
## [151] "15\t5\t0.0\t1\t5"
## [152] "16\t15\t0.0\t1\t12 3"
## [153] "17\t7\t0.0\t1\t6 1"
## [154] "18\t2\t0.0\t1\t2"
## [155] "19\t3\t0.0\t1\t2 1"
## [156] "20\t16\t0.0\t2\t13 3"
## [157] "21\t8\t0.0\t2\t6 2"
## [158] "22\t6\t0.0\t2\t2 2 2"
## [159] "23\t5\t0.0\t2\t3 1 1"
## [160] "24\t5\t0.0\t2\t3 2"
## [161] "25\t6\t0.0\t2\t5 0 1"
## [162] "26\t9\t0.0\t2\t6 3"
## [163] "27\t12\t0.0\t2\t7 5"
## [164] "28\t3\t0.0\t2\t2 1"
## [165] "30\t2\t0.0\t3\t0 1 0 1"
## [166] "31\t9\t0.0\t3\t4 2 1 2"
## [167] "32\t3\t0.0\t3\t3"
## [168] "33\t5\t0.0\t3\t3 2"
## [169] "34\t11\t0.0\t3\t9 2"
## [170] "35\t8\t0.0\t3\t7 1"
## [171] "36\t5\t0.0\t3\t2 1 2"
## [172] "37\t1\t0.0\t3\t1"
## [173] "38\t6\t0.0\t3\t4 2"
## [174] "39\t3\t0.0\t3\t0 1 1 1"
## [175] "40\t8\t0.0\t4\t4 0 2 1 1"
## [176] "41\t7\t0.0\t4\t5 2"
## [177] "42\t9\t0.0\t4\t6 2 1"
## [178] "43\t12\t0.0\t4\t9 2 0 1"
## [179] "44\t9\t0.0\t4\t7 2"
## [180] "45\t12\t0.0\t4\t10 2"
## [181] "46\t15\t0.0\t4\t8 5 1 1"
## [182] "47\t9\t0.0\t4\t5 3 0 1"
## [183] "48\t3\t0.0\t4\t2 1"
## [184] "49\t3\t0.0\t4\t1 1 1"
## [185] "50\t12\t0.0\t4\t8 3 0 1"
## [186] "51\t9\t0.0\t4\t5 3 0 1"
## [187] "52\t15\t0.0\t4\t7 4 3 0 1"
## [188] "53\t4\t0.0\t4\t3 0 0 0 1"
## [189] "54\t8\t0.0\t4\t6 2"
## [190] "55\t4\t0.0\t4\t1 2 0 1"
## [191] "56\t12\t0.0\t4\t9 2 0 0 1"
## [192] "57\t18\t0.0\t4\t9 5 1 1 2"
## [193] "58\t11\t0.0\t4\t8 1 0 1 1"
## [194] "59\t9\t0.0\t4\t7 1 1"
## [195] "60\t13\t0.0\t4\t8 5"
## [196] "61\t11\t0.0\t4\t7 3 1"
## [197] "62\t21\t0.0\t4\t17 2 2"
## [198] "63\t30\t0.0\t4\t24 3 3"
## [199] "64\t43\t0.0\t4\t34 6 2 0 1"
## [200] "65\t26\t0.0\t4\t18 7 0 1"
## [201] "66\t21\t0.0\t4\t16 3 2"
## [202] "67\t18\t0.0\t4\t17 1"
## [203] "68\t2\t0.0\t4\t2"
## [204] "69\t5\t0.0\t4\t3 2"
## [205] "70\t13\t0.0\t4\t11 1 1"
## [206] "71\t8\t0.0\t4\t4 4"
## [207] "72\t3\t0.0\t4\t3"
## [208] "73\t11\t0.0\t4\t9 2"
## [209] "74\t24\t0.0\t4\t17 6 0 0 1"
## [210] "75\t12\t0.0\t4\t10 1 1"
## [211] "76\t7\t0.0\t4\t5 2"
## [212] "77\t40\t0.0\t4\t34 5 0 1"
## [213] "78\t11\t0.0\t4\t8 3"
## [214] "79\t11\t0.0\t4\t7 4"
## [215] "80\t5\t0.0\t4\t3 1 1"
## [216] "81\t3\t0.0\t4\t3"
## [217] "82\t11\t0.0\t4\t7 3 1"
## [218] "83\t32\t0.0\t4\t30 2"
## [219] "84\t50\t0.0\t4\t44 5 0 0 1"
## [220] "85\t63\t0.0\t4\t52 9 0 2"
## [221] "86\t22\t0.0\t4\t12 8 2"
## [222] "87\t13\t0.0\t4\t10 3"
## [223] "88\t8\t0.0\t4\t5 3"
## [224] "89\t119\t0.0\t4\t20 78 14 6 1"
## [225] "90\t9\t0.0\t4\t4 5"
## [226] "91\t6\t0.0\t4\t5 1"
## [227] "92\t15\t0.0\t4\t13 2"
## [228] "93\t12\t0.0\t4\t9 3"
## [229] "94\t12\t0.0\t4\t8 4"
## [230] "95\t8\t0.0\t4\t7 1"
## [231] "96\t6\t0.0\t4\t6"
## [232] "97\t1\t0.0\t4\t1"
## [233] "98\t3\t0.0\t4\t2 1"
## [234] "99\t6\t0.0\t4\t6"
## [235] "100\t6\t0.0\t4\t5 1"
## [236] "101\t5\t0.0\t4\t4 1"
## [237] "102\t16\t0.0\t4\t16"
## [238] "103\t8\t0.0\t4\t7 1"
## [239] "104\t7\t0.0\t4\t7"
## [240] "105\t6\t0.0\t4\t2 2 2"
## [241] "106\t3\t0.0\t4\t3"
## [242] "107\t1\t0.0\t4\t1"
## [243] "108\t8\t0.0\t4\t5 2 1"
## [244] "109\t12\t0.0\t4\t4 8"
## [245] "110\t15\t0.0\t4\t7 7 1"
## [246] "111\t4\t0.0\t4\t4"
## [247] "112\t9\t0.0\t4\t8 1"
## [248] "113\t5\t0.0\t4\t4 1"
## [249] "114\t13\t0.0\t4\t12 1"
## [250] "115\t9\t0.0\t4\t8 1"
## [251] "116\t7\t0.0\t4\t5 2"
## [252] "117\t6\t0.0\t4\t5 1"
## [253] "118\t43\t0.0\t4\t20 21 2"
## [254] "119\t14\t0.0\t4\t10 4"
## [255] "120\t10\t0.0\t4\t7 2 0 1"
## [256] "121\t7\t0.0\t4\t6 0 1"
## [257] "122\t6\t0.0\t4\t5 1"
## [258] "123\t3\t0.0\t4\t2 1"
## [259] "124\t9\t0.0\t4\t9"
## [260] "125\t8\t0.0\t4\t7 1"
## [261] "126\t10\t0.0\t4\t9 1"
## [262] "127\t2\t0.0\t4\t2"
## [263] "128\t4\t0.0\t4\t4"
## [264] "129\t1\t0.0\t4\t1"
## [265] "130\t2\t0.0\t4\t1 1"
## [266] "131\t1\t0.0\t4\t1"
## [267] "132\t3\t0.0\t4\t3"
## [268] "133\t3\t0.0\t4\t3"
## [269] "134\t3\t0.0\t4\t2 0 1"
## [270] "135\t7\t0.0\t4\t6 1"
## [271] "136\t3\t0.0\t4\t2 0 1"
## [272] "137\t3\t0.0\t4\t2 1"
## [273] "138\t9\t0.0\t4\t9"
## [274] "139\t6\t0.0\t4\t3 3"
## [275] "140\t18\t0.0\t4\t16 2"
## [276] "141\t1\t0.0\t4\t1"
## [277] "142\t4\t0.0\t4\t3 1"
## [278] "143\t1\t0.0\t4\t0 1"
## [279] "145\t2\t0.0\t4\t2"
## [280] "146\t1\t0.0\t4\t1"
## [281] "147\t6\t0.0\t4\t5 1"
## [282] "148\t8\t0.0\t4\t8"
## [283] "149\t4\t0.0\t4\t4"
## [284] "150\t6\t0.0\t4\t5 1"
## [285] "151\t4\t0.0\t4\t4"
## [286] "152\t3\t0.0\t4\t2 0 1"
## [287] "153\t2\t0.0\t4\t2"
## [288] "154\t1\t0.0\t4\t0 1"
## [289] "157\t2\t0.0\t4\t1 1"
## [290] "159\t3\t0.0\t4\t1 1 0 1"
## [291] "160\t7\t0.0\t4\t5 2"
## [292] "161\t1\t0.0\t4\t1"
## [293] "162\t3\t0.0\t4\t3"
## [294] "163\t2\t0.0\t4\t1 1"
## [295] "164\t1\t0.0\t4\t1"
## [296] "165\t2\t0.0\t4\t2"
## [297] "166\t1\t0.0\t4\t1"
## [298] "167\t1\t0.0\t4\t0 1"
## [299] "169\t1\t0.0\t4\t1"
## [300] "170\t2\t0.0\t4\t2"
## [301] "171\t2\t0.0\t4\t2"
## [302] "172\t3\t0.0\t4\t3"
## [303] "173\t1\t0.0\t4\t1"
## [304] "175\t1\t0.0\t4\t0 1"
## [305] "176\t1\t0.0\t4\t1"
## [306] "180\t1\t0.0\t4\t1"
##
## [[21]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14BRNA3_S21_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14BRNA3_S21_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14BRNA3_S21_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14BRNA3_S21_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.95 s (110 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 8,665"
## [9] " Read 1 with adapter: 185 (2.1%)"
## [10] " Read 2 with adapter: 1,055 (12.2%)"
## [11] "Pairs written (passing filters): 8,663 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,639,300 bp"
## [14] " Read 1: 1,698,340 bp"
## [15] " Read 2: 1,940,960 bp"
## [16] "Total written (filtered): 3,544,949 bp (97.4%)"
## [17] " Read 1: 1,687,020 bp"
## [18] " Read 2: 1,857,929 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 20 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t8.5\t0\t1"
## [30] "8\t1\t0.1\t0\t1"
## [31] "16\t1\t0.0\t1\t1"
## [32] "17\t4\t0.0\t1\t3 1"
## [33] "31\t4\t0.0\t3\t4"
## [34] "32\t1\t0.0\t3\t0 0 1"
## [35] "33\t2\t0.0\t3\t2"
## [36] "34\t4\t0.0\t3\t4"
## [37] "36\t2\t0.0\t3\t2"
## [38] ""
## [39] ""
## [40] "=== First read: Adapter 2 ==="
## [41] ""
## [42] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 165 times"
## [43] ""
## [44] "No. of allowed errors:"
## [45] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [46] ""
## [47] "Bases preceding removed adapters:"
## [48] " A: 71.5%"
## [49] " C: 0.0%"
## [50] " G: 24.8%"
## [51] " T: 3.6%"
## [52] " none/other: 0.0%"
## [53] ""
## [54] "Overview of removed sequences"
## [55] "length\tcount\texpect\tmax.err\terror counts"
## [56] "5\t2\t8.5\t0\t2"
## [57] "6\t1\t2.1\t0\t1"
## [58] "8\t1\t0.1\t0\t1"
## [59] "13\t1\t0.0\t1\t1"
## [60] "17\t1\t0.0\t1\t1"
## [61] "24\t1\t0.0\t2\t1"
## [62] "29\t2\t0.0\t2\t2"
## [63] "36\t4\t0.0\t2\t4"
## [64] "40\t1\t0.0\t2\t1"
## [65] "43\t1\t0.0\t2\t1"
## [66] "48\t1\t0.0\t2\t1"
## [67] "54\t1\t0.0\t2\t1"
## [68] "55\t2\t0.0\t2\t2"
## [69] "56\t1\t0.0\t2\t1"
## [70] "59\t5\t0.0\t2\t5"
## [71] "60\t5\t0.0\t2\t5"
## [72] "61\t98\t0.0\t2\t92 5 1"
## [73] "62\t3\t0.0\t2\t3"
## [74] "65\t1\t0.0\t2\t1"
## [75] "74\t3\t0.0\t2\t3"
## [76] "80\t1\t0.0\t2\t1"
## [77] "81\t1\t0.0\t2\t1"
## [78] "82\t4\t0.0\t2\t4"
## [79] "90\t18\t0.0\t2\t17 1"
## [80] "96\t2\t0.0\t2\t2"
## [81] "98\t1\t0.0\t2\t1"
## [82] "106\t1\t0.0\t2\t1"
## [83] "108\t1\t0.0\t2\t1"
## [84] "111\t1\t0.0\t2\t1"
## [85] ""
## [86] ""
## [87] "=== Second read: Adapter 3 ==="
## [88] ""
## [89] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 7 times"
## [90] ""
## [91] "No. of allowed errors:"
## [92] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [93] ""
## [94] "Overview of removed sequences"
## [95] "length\tcount\texpect\tmax.err\terror counts"
## [96] "5\t1\t8.5\t0\t1"
## [97] "15\t1\t0.0\t1\t1"
## [98] "76\t1\t0.0\t2\t1"
## [99] "80\t1\t0.0\t2\t1"
## [100] "125\t3\t0.0\t2\t3"
## [101] ""
## [102] ""
## [103] "=== Second read: Adapter 4 ==="
## [104] ""
## [105] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 1049 times"
## [106] ""
## [107] "No. of allowed errors:"
## [108] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [109] ""
## [110] "Bases preceding removed adapters:"
## [111] " A: 43.9%"
## [112] " C: 8.1%"
## [113] " G: 47.9%"
## [114] " T: 0.1%"
## [115] " none/other: 0.0%"
## [116] ""
## [117] "Overview of removed sequences"
## [118] "length\tcount\texpect\tmax.err\terror counts"
## [119] "5\t5\t8.5\t0\t5"
## [120] "6\t6\t2.1\t0\t6"
## [121] "7\t4\t0.5\t0\t4"
## [122] "8\t9\t0.1\t0\t9"
## [123] "9\t6\t0.0\t0\t6"
## [124] "10\t4\t0.0\t1\t4"
## [125] "11\t2\t0.0\t1\t2"
## [126] "12\t2\t0.0\t1\t2"
## [127] "13\t5\t0.0\t1\t5"
## [128] "14\t11\t0.0\t1\t9 2"
## [129] "15\t8\t0.0\t1\t7 1"
## [130] "16\t11\t0.0\t1\t10 1"
## [131] "17\t5\t0.0\t1\t5"
## [132] "18\t3\t0.0\t1\t3"
## [133] "19\t3\t0.0\t1\t2 1"
## [134] "20\t10\t0.0\t2\t7 2 1"
## [135] "21\t3\t0.0\t2\t2 1"
## [136] "22\t9\t0.0\t2\t6 3"
## [137] "23\t2\t0.0\t2\t1 1"
## [138] "24\t3\t0.0\t2\t2 1"
## [139] "25\t2\t0.0\t2\t1 1"
## [140] "26\t4\t0.0\t2\t4"
## [141] "27\t2\t0.0\t2\t2"
## [142] "28\t4\t0.0\t2\t3 1"
## [143] "29\t2\t0.0\t2\t2"
## [144] "30\t7\t0.0\t3\t4 3"
## [145] "31\t7\t0.0\t3\t4 2 1"
## [146] "32\t6\t0.0\t3\t4 1 1"
## [147] "33\t6\t0.0\t3\t3 2 1"
## [148] "34\t5\t0.0\t3\t3 1 1"
## [149] "35\t7\t0.0\t3\t5 2"
## [150] "36\t6\t0.0\t3\t5 1"
## [151] "37\t1\t0.0\t3\t0 1"
## [152] "38\t3\t0.0\t3\t1 1 1"
## [153] "39\t3\t0.0\t3\t3"
## [154] "40\t5\t0.0\t4\t4 1"
## [155] "41\t10\t0.0\t4\t4 1 4 1"
## [156] "42\t6\t0.0\t4\t3 1 2"
## [157] "43\t14\t0.0\t4\t7 5 1 1"
## [158] "44\t3\t0.0\t4\t2 1"
## [159] "45\t12\t0.0\t4\t5 5 1 0 1"
## [160] "46\t14\t0.0\t4\t8 5 1"
## [161] "47\t2\t0.0\t4\t1 1"
## [162] "48\t1\t0.0\t4\t1"
## [163] "49\t1\t0.0\t4\t1"
## [164] "50\t9\t0.0\t4\t5 3 1"
## [165] "51\t4\t0.0\t4\t0 3 1"
## [166] "52\t11\t0.0\t4\t5 5 1"
## [167] "53\t5\t0.0\t4\t4 1"
## [168] "54\t7\t0.0\t4\t5 1 1"
## [169] "55\t7\t0.0\t4\t5 2"
## [170] "56\t7\t0.0\t4\t5 1 0 1"
## [171] "57\t6\t0.0\t4\t4 1 1"
## [172] "58\t6\t0.0\t4\t4 2"
## [173] "59\t7\t0.0\t4\t6 1"
## [174] "60\t5\t0.0\t4\t4 0 0 1"
## [175] "61\t2\t0.0\t4\t1 1"
## [176] "62\t14\t0.0\t4\t12 1 1"
## [177] "63\t10\t0.0\t4\t7 3"
## [178] "64\t23\t0.0\t4\t16 6 0 1"
## [179] "65\t16\t0.0\t4\t12 1 1 1 1"
## [180] "66\t19\t0.0\t4\t16 3"
## [181] "67\t8\t0.0\t4\t5 1 2"
## [182] "68\t4\t0.0\t4\t4"
## [183] "69\t4\t0.0\t4\t2 2"
## [184] "71\t4\t0.0\t4\t3 1"
## [185] "72\t3\t0.0\t4\t2 1"
## [186] "73\t2\t0.0\t4\t1 1"
## [187] "74\t9\t0.0\t4\t6 3"
## [188] "75\t7\t0.0\t4\t5 2"
## [189] "76\t5\t0.0\t4\t4 1"
## [190] "77\t14\t0.0\t4\t10 4"
## [191] "78\t9\t0.0\t4\t8 1"
## [192] "79\t9\t0.0\t4\t7 2"
## [193] "80\t4\t0.0\t4\t4"
## [194] "81\t5\t0.0\t4\t5"
## [195] "82\t8\t0.0\t4\t7 1"
## [196] "83\t29\t0.0\t4\t25 3 1"
## [197] "84\t30\t0.0\t4\t28 2"
## [198] "85\t30\t0.0\t4\t26 3 1"
## [199] "86\t16\t0.0\t4\t12 3 1"
## [200] "87\t13\t0.0\t4\t6 5 2"
## [201] "88\t7\t0.0\t4\t3 3 1"
## [202] "89\t101\t0.0\t4\t13 73 13 2"
## [203] "90\t7\t0.0\t4\t6 1"
## [204] "91\t7\t0.0\t4\t5 1 1"
## [205] "92\t8\t0.0\t4\t4 4"
## [206] "93\t7\t0.0\t4\t5 2"
## [207] "94\t13\t0.0\t4\t8 5"
## [208] "95\t8\t0.0\t4\t3 4 1"
## [209] "96\t6\t0.0\t4\t6"
## [210] "97\t4\t0.0\t4\t3 0 1"
## [211] "98\t3\t0.0\t4\t2 1"
## [212] "99\t1\t0.0\t4\t1"
## [213] "100\t1\t0.0\t4\t0 1"
## [214] "101\t4\t0.0\t4\t4"
## [215] "102\t10\t0.0\t4\t10"
## [216] "103\t8\t0.0\t4\t7 0 1"
## [217] "104\t6\t0.0\t4\t6"
## [218] "105\t2\t0.0\t4\t2"
## [219] "106\t2\t0.0\t4\t1 1"
## [220] "108\t4\t0.0\t4\t3 1"
## [221] "109\t7\t0.0\t4\t6 1"
## [222] "110\t13\t0.0\t4\t8 5"
## [223] "111\t1\t0.0\t4\t1"
## [224] "112\t10\t0.0\t4\t6 4"
## [225] "113\t4\t0.0\t4\t3 1"
## [226] "114\t5\t0.0\t4\t5"
## [227] "115\t7\t0.0\t4\t6 1"
## [228] "116\t3\t0.0\t4\t3"
## [229] "117\t4\t0.0\t4\t3 1"
## [230] "118\t20\t0.0\t4\t12 8"
## [231] "119\t12\t0.0\t4\t11 0 0 0 1"
## [232] "120\t5\t0.0\t4\t4 1"
## [233] "121\t1\t0.0\t4\t1"
## [234] "122\t2\t0.0\t4\t2"
## [235] "123\t3\t0.0\t4\t3"
## [236] "124\t4\t0.0\t4\t2 1 1"
## [237] "125\t5\t0.0\t4\t2 2 1"
## [238] "126\t3\t0.0\t4\t2 1"
## [239] "127\t4\t0.0\t4\t3 1"
## [240] "128\t2\t0.0\t4\t2"
## [241] "129\t3\t0.0\t4\t2 1"
## [242] "130\t1\t0.0\t4\t1"
## [243] "131\t2\t0.0\t4\t1 1"
## [244] "132\t2\t0.0\t4\t2"
## [245] "133\t1\t0.0\t4\t1"
## [246] "134\t2\t0.0\t4\t2"
## [247] "135\t2\t0.0\t4\t2"
## [248] "136\t1\t0.0\t4\t0 1"
## [249] "137\t2\t0.0\t4\t2"
## [250] "138\t8\t0.0\t4\t6 1 1"
## [251] "139\t8\t0.0\t4\t7 1"
## [252] "140\t5\t0.0\t4\t4 1"
## [253] "141\t6\t0.0\t4\t6"
## [254] "142\t3\t0.0\t4\t3"
## [255] "143\t2\t0.0\t4\t2"
## [256] "144\t3\t0.0\t4\t3"
## [257] "145\t2\t0.0\t4\t2"
## [258] "146\t4\t0.0\t4\t4"
## [259] "147\t3\t0.0\t4\t1 2"
## [260] "148\t4\t0.0\t4\t4"
## [261] "149\t2\t0.0\t4\t2"
## [262] "150\t5\t0.0\t4\t5"
## [263] "151\t1\t0.0\t4\t0 1"
## [264] "152\t2\t0.0\t4\t0 2"
## [265] "153\t2\t0.0\t4\t1 1"
## [266] "154\t4\t0.0\t4\t3 0 1"
## [267] "155\t3\t0.0\t4\t2 1"
## [268] "158\t4\t0.0\t4\t3 1"
## [269] "160\t4\t0.0\t4\t3 1"
## [270] "161\t3\t0.0\t4\t2 1"
## [271] "162\t4\t0.0\t4\t3 1"
## [272] "163\t1\t0.0\t4\t0 1"
## [273] "164\t1\t0.0\t4\t0 1"
## [274] "165\t3\t0.0\t4\t2 1"
## [275] "166\t1\t0.0\t4\t1"
## [276] "172\t3\t0.0\t4\t3"
## [277] "174\t1\t0.0\t4\t1"
## [278] "177\t1\t0.0\t4\t0 1"
## [279] "179\t1\t0.0\t4\t1"
##
## [[22]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14BRNA4_S22_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14BRNA4_S22_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14BRNA4_S22_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14BRNA4_S22_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.46 s (111 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 4,121"
## [9] " Read 1 with adapter: 34 (0.8%)"
## [10] " Read 2 with adapter: 141 (3.4%)"
## [11] "Pairs written (passing filters): 4,119 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 1,730,820 bp"
## [14] " Read 1: 807,716 bp"
## [15] " Read 2: 923,104 bp"
## [16] "Total written (filtered): 1,718,599 bp (99.3%)"
## [17] " Read 1: 805,626 bp"
## [18] " Read 2: 912,973 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 1 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "31\t1\t0.0\t3\t1"
## [30] ""
## [31] ""
## [32] "=== First read: Adapter 2 ==="
## [33] ""
## [34] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 33 times"
## [35] ""
## [36] "No. of allowed errors:"
## [37] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [38] ""
## [39] "Bases preceding removed adapters:"
## [40] " A: 66.7%"
## [41] " C: 0.0%"
## [42] " G: 33.3%"
## [43] " T: 0.0%"
## [44] " none/other: 0.0%"
## [45] ""
## [46] "Overview of removed sequences"
## [47] "length\tcount\texpect\tmax.err\terror counts"
## [48] "5\t3\t4.0\t0\t3"
## [49] "8\t2\t0.1\t0\t2"
## [50] "10\t1\t0.0\t1\t1"
## [51] "12\t1\t0.0\t1\t1"
## [52] "27\t1\t0.0\t2\t1"
## [53] "30\t1\t0.0\t2\t1"
## [54] "31\t1\t0.0\t2\t1"
## [55] "34\t1\t0.0\t2\t1"
## [56] "43\t1\t0.0\t2\t1"
## [57] "45\t1\t0.0\t2\t1"
## [58] "55\t1\t0.0\t2\t1"
## [59] "61\t14\t0.0\t2\t14"
## [60] "71\t1\t0.0\t2\t1"
## [61] "73\t1\t0.0\t2\t1"
## [62] "90\t1\t0.0\t2\t1"
## [63] "116\t1\t0.0\t2\t1"
## [64] "145\t1\t0.0\t2\t1"
## [65] ""
## [66] ""
## [67] "=== Second read: Adapter 3 ==="
## [68] ""
## [69] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [70] ""
## [71] "=== Second read: Adapter 4 ==="
## [72] ""
## [73] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 141 times"
## [74] ""
## [75] "No. of allowed errors:"
## [76] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [77] ""
## [78] "Bases preceding removed adapters:"
## [79] " A: 53.2%"
## [80] " C: 11.3%"
## [81] " G: 35.5%"
## [82] " T: 0.0%"
## [83] " none/other: 0.0%"
## [84] ""
## [85] "Overview of removed sequences"
## [86] "length\tcount\texpect\tmax.err\terror counts"
## [87] "5\t1\t4.0\t0\t1"
## [88] "6\t1\t1.0\t0\t1"
## [89] "8\t2\t0.1\t0\t2"
## [90] "10\t1\t0.0\t1\t1"
## [91] "13\t1\t0.0\t1\t0 1"
## [92] "14\t2\t0.0\t1\t2"
## [93] "15\t2\t0.0\t1\t1 1"
## [94] "16\t2\t0.0\t1\t1 1"
## [95] "20\t3\t0.0\t2\t3"
## [96] "22\t3\t0.0\t2\t2 1"
## [97] "27\t1\t0.0\t2\t0 1"
## [98] "30\t2\t0.0\t3\t1 1"
## [99] "31\t2\t0.0\t3\t1 0 1"
## [100] "33\t4\t0.0\t3\t2 1 0 1"
## [101] "34\t1\t0.0\t3\t1"
## [102] "35\t3\t0.0\t3\t1 2"
## [103] "36\t2\t0.0\t3\t2"
## [104] "38\t2\t0.0\t3\t1 0 0 1"
## [105] "39\t3\t0.0\t3\t2 1"
## [106] "40\t1\t0.0\t4\t0 0 1"
## [107] "41\t1\t0.0\t4\t1"
## [108] "42\t1\t0.0\t4\t1"
## [109] "43\t1\t0.0\t4\t0 0 1"
## [110] "44\t2\t0.0\t4\t2"
## [111] "45\t1\t0.0\t4\t1"
## [112] "46\t2\t0.0\t4\t0 2"
## [113] "47\t2\t0.0\t4\t1 1"
## [114] "51\t2\t0.0\t4\t1 1"
## [115] "52\t2\t0.0\t4\t2"
## [116] "53\t1\t0.0\t4\t1"
## [117] "54\t1\t0.0\t4\t0 1"
## [118] "56\t1\t0.0\t4\t0 1"
## [119] "57\t1\t0.0\t4\t1"
## [120] "58\t2\t0.0\t4\t2"
## [121] "59\t5\t0.0\t4\t3 2"
## [122] "60\t2\t0.0\t4\t2"
## [123] "62\t1\t0.0\t4\t0 1"
## [124] "63\t3\t0.0\t4\t3"
## [125] "65\t1\t0.0\t4\t0 1"
## [126] "66\t1\t0.0\t4\t1"
## [127] "70\t1\t0.0\t4\t0 1"
## [128] "71\t1\t0.0\t4\t1"
## [129] "72\t1\t0.0\t4\t0 1"
## [130] "73\t3\t0.0\t4\t2 1"
## [131] "75\t1\t0.0\t4\t1"
## [132] "77\t2\t0.0\t4\t1 1"
## [133] "78\t1\t0.0\t4\t1"
## [134] "79\t1\t0.0\t4\t1"
## [135] "80\t1\t0.0\t4\t1"
## [136] "82\t1\t0.0\t4\t1"
## [137] "83\t1\t0.0\t4\t0 1"
## [138] "85\t2\t0.0\t4\t1 0 0 0 1"
## [139] "89\t15\t0.0\t4\t0 12 2 1"
## [140] "91\t1\t0.0\t4\t1"
## [141] "92\t2\t0.0\t4\t1 1"
## [142] "94\t1\t0.0\t4\t1"
## [143] "97\t1\t0.0\t4\t0 1"
## [144] "101\t1\t0.0\t4\t1"
## [145] "102\t1\t0.0\t4\t1"
## [146] "103\t2\t0.0\t4\t1 1"
## [147] "105\t1\t0.0\t4\t1"
## [148] "106\t2\t0.0\t4\t2"
## [149] "108\t1\t0.0\t4\t1"
## [150] "110\t2\t0.0\t4\t1 1"
## [151] "111\t2\t0.0\t4\t2"
## [152] "115\t1\t0.0\t4\t1"
## [153] "116\t3\t0.0\t4\t2 1"
## [154] "117\t1\t0.0\t4\t1"
## [155] "118\t1\t0.0\t4\t0 0 1"
## [156] "127\t2\t0.0\t4\t1 0 0 0 1"
## [157] "130\t1\t0.0\t4\t1"
## [158] "134\t1\t0.0\t4\t1"
## [159] "141\t1\t0.0\t4\t1"
## [160] "144\t2\t0.0\t4\t1 1"
## [161] "148\t1\t0.0\t4\t1"
## [162] "149\t1\t0.0\t4\t1"
## [163] "150\t1\t0.0\t4\t1"
## [164] "160\t1\t0.0\t4\t0 1"
## [165] "173\t2\t0.0\t4\t1 1"
## [166] "180\t1\t0.0\t4\t1"
## [167] "194\t1\t0.0\t4\t1"
##
## [[23]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14C1_S23_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14C1_S23_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14C1_S23_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14C1_S23_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.26 s (106 us/read; 0.57 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 11,911"
## [9] " Read 1 with adapter: 5 (0.0%)"
## [10] " Read 2 with adapter: 187 (1.6%)"
## [11] "Pairs written (passing filters): 11,911 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 5,002,620 bp"
## [14] " Read 1: 2,334,556 bp"
## [15] " Read 2: 2,668,064 bp"
## [16] "Total written (filtered): 4,990,066 bp (99.7%)"
## [17] " Read 1: 2,334,490 bp"
## [18] " Read 2: 2,655,576 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 5 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t11.6\t0\t1"
## [30] "6\t1\t2.9\t0\t1"
## [31] "7\t1\t0.7\t0\t1"
## [32] "22\t1\t0.0\t2\t1"
## [33] "26\t1\t0.0\t2\t0 0 1"
## [34] ""
## [35] ""
## [36] "=== First read: Adapter 2 ==="
## [37] ""
## [38] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 0 times"
## [39] ""
## [40] "=== Second read: Adapter 3 ==="
## [41] ""
## [42] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [43] ""
## [44] "=== Second read: Adapter 4 ==="
## [45] ""
## [46] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 187 times"
## [47] ""
## [48] "No. of allowed errors:"
## [49] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [50] ""
## [51] "Bases preceding removed adapters:"
## [52] " A: 66.3%"
## [53] " C: 11.2%"
## [54] " G: 22.5%"
## [55] " T: 0.0%"
## [56] " none/other: 0.0%"
## [57] ""
## [58] "Overview of removed sequences"
## [59] "length\tcount\texpect\tmax.err\terror counts"
## [60] "5\t7\t11.6\t0\t7"
## [61] "6\t1\t2.9\t0\t1"
## [62] "7\t1\t0.7\t0\t1"
## [63] "8\t4\t0.2\t0\t4"
## [64] "9\t1\t0.0\t0\t1"
## [65] "10\t1\t0.0\t1\t1"
## [66] "11\t1\t0.0\t1\t1"
## [67] "12\t2\t0.0\t1\t1 1"
## [68] "13\t1\t0.0\t1\t1"
## [69] "14\t3\t0.0\t1\t3"
## [70] "15\t1\t0.0\t1\t1"
## [71] "16\t5\t0.0\t1\t5"
## [72] "17\t2\t0.0\t1\t2"
## [73] "18\t2\t0.0\t1\t2"
## [74] "22\t2\t0.0\t2\t2"
## [75] "23\t1\t0.0\t2\t1"
## [76] "24\t1\t0.0\t2\t1"
## [77] "25\t1\t0.0\t2\t1"
## [78] "27\t1\t0.0\t2\t1"
## [79] "30\t1\t0.0\t3\t1"
## [80] "31\t1\t0.0\t3\t1"
## [81] "33\t4\t0.0\t3\t4"
## [82] "34\t2\t0.0\t3\t2"
## [83] "35\t1\t0.0\t3\t1"
## [84] "36\t4\t0.0\t3\t3 1"
## [85] "37\t2\t0.0\t3\t2"
## [86] "39\t1\t0.0\t3\t1"
## [87] "40\t3\t0.0\t4\t3"
## [88] "42\t1\t0.0\t4\t1"
## [89] "43\t3\t0.0\t4\t3"
## [90] "44\t2\t0.0\t4\t1 1"
## [91] "45\t3\t0.0\t4\t1 2"
## [92] "46\t2\t0.0\t4\t0 2"
## [93] "47\t2\t0.0\t4\t2"
## [94] "50\t1\t0.0\t4\t1"
## [95] "51\t5\t0.0\t4\t5"
## [96] "52\t2\t0.0\t4\t1 1"
## [97] "55\t1\t0.0\t4\t1"
## [98] "56\t3\t0.0\t4\t3"
## [99] "57\t3\t0.0\t4\t3"
## [100] "60\t1\t0.0\t4\t1"
## [101] "62\t1\t0.0\t4\t1"
## [102] "63\t1\t0.0\t4\t1"
## [103] "64\t2\t0.0\t4\t2"
## [104] "65\t3\t0.0\t4\t3"
## [105] "67\t1\t0.0\t4\t1"
## [106] "69\t1\t0.0\t4\t1"
## [107] "70\t5\t0.0\t4\t4 1"
## [108] "72\t2\t0.0\t4\t1 1"
## [109] "73\t3\t0.0\t4\t3"
## [110] "74\t2\t0.0\t4\t2"
## [111] "76\t2\t0.0\t4\t2"
## [112] "77\t2\t0.0\t4\t2"
## [113] "78\t1\t0.0\t4\t1"
## [114] "80\t1\t0.0\t4\t1"
## [115] "81\t1\t0.0\t4\t1"
## [116] "82\t1\t0.0\t4\t1"
## [117] "83\t3\t0.0\t4\t3"
## [118] "84\t5\t0.0\t4\t5"
## [119] "85\t2\t0.0\t4\t0 1 1"
## [120] "86\t4\t0.0\t4\t4"
## [121] "87\t4\t0.0\t4\t4"
## [122] "89\t1\t0.0\t4\t0 1"
## [123] "90\t1\t0.0\t4\t1"
## [124] "92\t1\t0.0\t4\t1"
## [125] "93\t3\t0.0\t4\t3"
## [126] "94\t3\t0.0\t4\t3"
## [127] "95\t1\t0.0\t4\t1"
## [128] "97\t2\t0.0\t4\t2"
## [129] "100\t1\t0.0\t4\t0 1"
## [130] "101\t1\t0.0\t4\t1"
## [131] "102\t1\t0.0\t4\t1"
## [132] "103\t2\t0.0\t4\t2"
## [133] "104\t1\t0.0\t4\t1"
## [134] "105\t6\t0.0\t4\t5 1"
## [135] "106\t1\t0.0\t4\t1"
## [136] "112\t1\t0.0\t4\t1"
## [137] "113\t2\t0.0\t4\t2"
## [138] "114\t2\t0.0\t4\t2"
## [139] "116\t1\t0.0\t4\t1"
## [140] "117\t1\t0.0\t4\t1"
## [141] "119\t1\t0.0\t4\t1"
## [142] "122\t1\t0.0\t4\t1"
## [143] "124\t1\t0.0\t4\t1"
## [144] "125\t2\t0.0\t4\t2"
## [145] "126\t1\t0.0\t4\t1"
## [146] "127\t3\t0.0\t4\t2 1"
## [147] "128\t2\t0.0\t4\t2"
## [148] "138\t1\t0.0\t4\t1"
## [149] "139\t1\t0.0\t4\t1"
## [150] "140\t1\t0.0\t4\t1"
## [151] "146\t1\t0.0\t4\t1"
## [152] "147\t1\t0.0\t4\t1"
## [153] "148\t2\t0.0\t4\t2"
## [154] "149\t2\t0.0\t4\t2"
## [155] "160\t1\t0.0\t4\t1"
## [156] "161\t1\t0.0\t4\t1"
##
## [[24]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14C2_S24_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14C2_S24_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14C2_S24_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14C2_S24_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.48 s (105 us/read; 0.57 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 14,079"
## [9] " Read 1 with adapter: 8 (0.1%)"
## [10] " Read 2 with adapter: 217 (1.5%)"
## [11] "Pairs written (passing filters): 14,079 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 5,913,180 bp"
## [14] " Read 1: 2,759,484 bp"
## [15] " Read 2: 3,153,696 bp"
## [16] "Total written (filtered): 5,899,961 bp (99.8%)"
## [17] " Read 1: 2,759,402 bp"
## [18] " Read 2: 3,140,559 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 7 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t13.7\t0\t1"
## [30] "6\t1\t3.4\t0\t1"
## [31] "7\t1\t0.9\t0\t1"
## [32] "8\t1\t0.2\t0\t1"
## [33] "15\t1\t0.0\t1\t0 1"
## [34] "16\t1\t0.0\t1\t1"
## [35] "20\t1\t0.0\t2\t0 1"
## [36] ""
## [37] ""
## [38] "=== First read: Adapter 2 ==="
## [39] ""
## [40] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 1 times"
## [41] ""
## [42] "No. of allowed errors:"
## [43] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [44] ""
## [45] "Bases preceding removed adapters:"
## [46] " A: 100.0%"
## [47] " C: 0.0%"
## [48] " G: 0.0%"
## [49] " T: 0.0%"
## [50] " none/other: 0.0%"
## [51] ""
## [52] "Overview of removed sequences"
## [53] "length\tcount\texpect\tmax.err\terror counts"
## [54] "5\t1\t13.7\t0\t1"
## [55] ""
## [56] ""
## [57] "=== Second read: Adapter 3 ==="
## [58] ""
## [59] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [60] ""
## [61] "No. of allowed errors:"
## [62] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [63] ""
## [64] "Overview of removed sequences"
## [65] "length\tcount\texpect\tmax.err\terror counts"
## [66] "22\t1\t0.0\t2\t1"
## [67] ""
## [68] ""
## [69] "=== Second read: Adapter 4 ==="
## [70] ""
## [71] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 216 times"
## [72] ""
## [73] "No. of allowed errors:"
## [74] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [75] ""
## [76] "Bases preceding removed adapters:"
## [77] " A: 48.1%"
## [78] " C: 30.1%"
## [79] " G: 21.8%"
## [80] " T: 0.0%"
## [81] " none/other: 0.0%"
## [82] ""
## [83] "Overview of removed sequences"
## [84] "length\tcount\texpect\tmax.err\terror counts"
## [85] "6\t2\t3.4\t0\t2"
## [86] "7\t2\t0.9\t0\t2"
## [87] "8\t5\t0.2\t0\t5"
## [88] "9\t2\t0.1\t0\t2"
## [89] "12\t1\t0.0\t1\t1"
## [90] "13\t3\t0.0\t1\t3"
## [91] "14\t9\t0.0\t1\t8 1"
## [92] "16\t12\t0.0\t1\t10 2"
## [93] "17\t4\t0.0\t1\t2 2"
## [94] "18\t4\t0.0\t1\t4"
## [95] "19\t4\t0.0\t1\t0 4"
## [96] "20\t2\t0.0\t2\t1 0 1"
## [97] "21\t2\t0.0\t2\t2"
## [98] "22\t1\t0.0\t2\t1"
## [99] "25\t5\t0.0\t2\t5"
## [100] "26\t3\t0.0\t2\t3"
## [101] "27\t1\t0.0\t2\t0 0 1"
## [102] "28\t3\t0.0\t2\t1 1 1"
## [103] "29\t2\t0.0\t2\t2"
## [104] "30\t2\t0.0\t3\t1 1"
## [105] "31\t2\t0.0\t3\t2"
## [106] "32\t1\t0.0\t3\t1"
## [107] "33\t3\t0.0\t3\t2 1"
## [108] "34\t2\t0.0\t3\t2"
## [109] "35\t2\t0.0\t3\t0 2"
## [110] "39\t4\t0.0\t3\t2 2"
## [111] "40\t2\t0.0\t4\t2"
## [112] "41\t3\t0.0\t4\t2 1"
## [113] "42\t3\t0.0\t4\t2 0 0 1"
## [114] "44\t2\t0.0\t4\t1 1"
## [115] "45\t1\t0.0\t4\t1"
## [116] "46\t2\t0.0\t4\t2"
## [117] "47\t1\t0.0\t4\t1"
## [118] "48\t1\t0.0\t4\t1"
## [119] "50\t2\t0.0\t4\t2"
## [120] "51\t2\t0.0\t4\t1 1"
## [121] "52\t3\t0.0\t4\t3"
## [122] "53\t1\t0.0\t4\t1"
## [123] "54\t1\t0.0\t4\t1"
## [124] "55\t2\t0.0\t4\t1 0 0 1"
## [125] "56\t2\t0.0\t4\t2"
## [126] "58\t1\t0.0\t4\t1"
## [127] "60\t2\t0.0\t4\t2"
## [128] "62\t1\t0.0\t4\t1"
## [129] "63\t1\t0.0\t4\t1"
## [130] "64\t4\t0.0\t4\t4"
## [131] "65\t2\t0.0\t4\t2"
## [132] "66\t2\t0.0\t4\t2"
## [133] "67\t3\t0.0\t4\t2 0 0 0 1"
## [134] "68\t1\t0.0\t4\t0 1"
## [135] "72\t2\t0.0\t4\t2"
## [136] "73\t2\t0.0\t4\t2"
## [137] "74\t3\t0.0\t4\t3"
## [138] "75\t2\t0.0\t4\t2"
## [139] "76\t3\t0.0\t4\t3"
## [140] "77\t2\t0.0\t4\t2"
## [141] "79\t2\t0.0\t4\t2"
## [142] "80\t1\t0.0\t4\t1"
## [143] "82\t3\t0.0\t4\t2 1"
## [144] "83\t2\t0.0\t4\t2"
## [145] "84\t3\t0.0\t4\t3"
## [146] "85\t3\t0.0\t4\t3"
## [147] "86\t4\t0.0\t4\t3 1"
## [148] "87\t1\t0.0\t4\t1"
## [149] "88\t2\t0.0\t4\t2"
## [150] "90\t1\t0.0\t4\t1"
## [151] "93\t2\t0.0\t4\t2"
## [152] "94\t5\t0.0\t4\t4 1"
## [153] "98\t2\t0.0\t4\t2"
## [154] "101\t3\t0.0\t4\t3"
## [155] "102\t1\t0.0\t4\t1"
## [156] "103\t1\t0.0\t4\t1"
## [157] "104\t2\t0.0\t4\t2"
## [158] "105\t3\t0.0\t4\t3"
## [159] "106\t1\t0.0\t4\t1"
## [160] "107\t3\t0.0\t4\t3"
## [161] "109\t1\t0.0\t4\t1"
## [162] "111\t1\t0.0\t4\t1"
## [163] "112\t1\t0.0\t4\t1"
## [164] "113\t2\t0.0\t4\t1 1"
## [165] "118\t2\t0.0\t4\t2"
## [166] "119\t2\t0.0\t4\t2"
## [167] "120\t1\t0.0\t4\t1"
## [168] "123\t2\t0.0\t4\t2"
## [169] "124\t2\t0.0\t4\t2"
## [170] "125\t1\t0.0\t4\t1"
## [171] "126\t1\t0.0\t4\t1"
## [172] "129\t1\t0.0\t4\t1"
## [173] "134\t1\t0.0\t4\t1"
## [174] "137\t1\t0.0\t4\t1"
## [175] "138\t1\t0.0\t4\t1"
## [176] "139\t1\t0.0\t4\t1"
## [177] "140\t1\t0.0\t4\t1"
## [178] "142\t1\t0.0\t4\t1"
## [179] "147\t1\t0.0\t4\t1"
## [180] "148\t1\t0.0\t4\t1"
## [181] "151\t2\t0.0\t4\t2"
## [182] "167\t1\t0.0\t4\t1"
## [183] "169\t1\t0.0\t4\t1"
##
## [[25]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14C3_S25_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14C3_S25_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14C3_S25_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14C3_S25_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.02 s (110 us/read; 0.55 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 9,283"
## [9] " Read 1 with adapter: 42 (0.5%)"
## [10] " Read 2 with adapter: 355 (3.8%)"
## [11] "Pairs written (passing filters): 9,282 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,898,860 bp"
## [14] " Read 1: 1,819,468 bp"
## [15] " Read 2: 2,079,392 bp"
## [16] "Total written (filtered): 3,873,183 bp (99.3%)"
## [17] " Read 1: 1,818,283 bp"
## [18] " Read 2: 2,054,900 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 40 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "7\t1\t0.6\t0\t1"
## [30] "16\t1\t0.0\t1\t0 1"
## [31] "17\t27\t0.0\t1\t27"
## [32] "30\t1\t0.0\t3\t1"
## [33] "31\t7\t0.0\t3\t6 1"
## [34] "48\t2\t0.0\t4\t0 0 2"
## [35] "71\t1\t0.0\t4\t0 0 0 1"
## [36] ""
## [37] ""
## [38] "=== First read: Adapter 2 ==="
## [39] ""
## [40] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 2 times"
## [41] ""
## [42] "No. of allowed errors:"
## [43] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [44] ""
## [45] "Bases preceding removed adapters:"
## [46] " A: 0.0%"
## [47] " C: 0.0%"
## [48] " G: 100.0%"
## [49] " T: 0.0%"
## [50] " none/other: 0.0%"
## [51] ""
## [52] "Overview of removed sequences"
## [53] "length\tcount\texpect\tmax.err\terror counts"
## [54] "72\t1\t0.0\t2\t0 1"
## [55] "92\t1\t0.0\t2\t1"
## [56] ""
## [57] ""
## [58] "=== Second read: Adapter 3 ==="
## [59] ""
## [60] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [61] ""
## [62] "No. of allowed errors:"
## [63] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [64] ""
## [65] "Overview of removed sequences"
## [66] "length\tcount\texpect\tmax.err\terror counts"
## [67] "31\t1\t0.0\t2\t1"
## [68] ""
## [69] ""
## [70] "=== Second read: Adapter 4 ==="
## [71] ""
## [72] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 354 times"
## [73] ""
## [74] "No. of allowed errors:"
## [75] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [76] ""
## [77] "Bases preceding removed adapters:"
## [78] " A: 56.8%"
## [79] " C: 12.1%"
## [80] " G: 30.8%"
## [81] " T: 0.3%"
## [82] " none/other: 0.0%"
## [83] ""
## [84] "Overview of removed sequences"
## [85] "length\tcount\texpect\tmax.err\terror counts"
## [86] "5\t2\t9.1\t0\t2"
## [87] "6\t2\t2.3\t0\t2"
## [88] "7\t4\t0.6\t0\t4"
## [89] "8\t1\t0.1\t0\t1"
## [90] "9\t1\t0.0\t0\t1"
## [91] "11\t2\t0.0\t1\t1 1"
## [92] "12\t1\t0.0\t1\t1"
## [93] "13\t4\t0.0\t1\t4"
## [94] "14\t6\t0.0\t1\t6"
## [95] "15\t3\t0.0\t1\t3"
## [96] "16\t7\t0.0\t1\t7"
## [97] "17\t2\t0.0\t1\t2"
## [98] "18\t2\t0.0\t1\t2"
## [99] "19\t1\t0.0\t1\t1"
## [100] "20\t1\t0.0\t2\t1"
## [101] "21\t4\t0.0\t2\t4"
## [102] "22\t7\t0.0\t2\t6 1"
## [103] "23\t4\t0.0\t2\t3 1"
## [104] "24\t4\t0.0\t2\t3 1"
## [105] "25\t1\t0.0\t2\t1"
## [106] "26\t3\t0.0\t2\t3"
## [107] "27\t3\t0.0\t2\t2 1"
## [108] "28\t2\t0.0\t2\t1 1"
## [109] "30\t2\t0.0\t3\t1 0 1"
## [110] "31\t2\t0.0\t3\t2"
## [111] "32\t2\t0.0\t3\t2"
## [112] "33\t3\t0.0\t3\t3"
## [113] "34\t3\t0.0\t3\t2 1"
## [114] "35\t4\t0.0\t3\t4"
## [115] "36\t1\t0.0\t3\t1"
## [116] "37\t1\t0.0\t3\t0 0 1"
## [117] "38\t2\t0.0\t3\t2"
## [118] "39\t5\t0.0\t3\t2 2 1"
## [119] "40\t1\t0.0\t4\t1"
## [120] "41\t2\t0.0\t4\t1 0 1"
## [121] "42\t1\t0.0\t4\t1"
## [122] "43\t5\t0.0\t4\t3 1 0 1"
## [123] "44\t2\t0.0\t4\t2"
## [124] "45\t4\t0.0\t4\t2 2"
## [125] "46\t6\t0.0\t4\t2 3 0 1"
## [126] "47\t3\t0.0\t4\t2 1"
## [127] "49\t2\t0.0\t4\t2"
## [128] "50\t4\t0.0\t4\t2 1 0 0 1"
## [129] "51\t5\t0.0\t4\t5"
## [130] "52\t3\t0.0\t4\t3"
## [131] "53\t2\t0.0\t4\t2"
## [132] "54\t3\t0.0\t4\t3"
## [133] "55\t2\t0.0\t4\t2"
## [134] "56\t2\t0.0\t4\t2"
## [135] "57\t6\t0.0\t4\t5 1"
## [136] "58\t4\t0.0\t4\t3 0 1"
## [137] "59\t3\t0.0\t4\t3"
## [138] "60\t1\t0.0\t4\t1"
## [139] "61\t2\t0.0\t4\t2"
## [140] "62\t5\t0.0\t4\t5"
## [141] "63\t6\t0.0\t4\t5 1"
## [142] "64\t4\t0.0\t4\t4"
## [143] "65\t5\t0.0\t4\t3 1 0 0 1"
## [144] "66\t7\t0.0\t4\t6 0 1"
## [145] "67\t4\t0.0\t4\t4"
## [146] "68\t3\t0.0\t4\t3"
## [147] "69\t2\t0.0\t4\t2"
## [148] "70\t2\t0.0\t4\t2"
## [149] "72\t2\t0.0\t4\t1 1"
## [150] "73\t5\t0.0\t4\t4 1"
## [151] "74\t2\t0.0\t4\t1 1"
## [152] "75\t2\t0.0\t4\t2"
## [153] "76\t4\t0.0\t4\t3 1"
## [154] "77\t4\t0.0\t4\t2 2"
## [155] "78\t1\t0.0\t4\t0 1"
## [156] "79\t4\t0.0\t4\t4"
## [157] "80\t4\t0.0\t4\t4"
## [158] "81\t1\t0.0\t4\t1"
## [159] "82\t5\t0.0\t4\t4 1"
## [160] "83\t3\t0.0\t4\t2 1"
## [161] "84\t8\t0.0\t4\t7 1"
## [162] "85\t6\t0.0\t4\t5 1"
## [163] "86\t4\t0.0\t4\t3 1"
## [164] "87\t3\t0.0\t4\t2 0 0 1"
## [165] "88\t1\t0.0\t4\t1"
## [166] "89\t4\t0.0\t4\t4"
## [167] "92\t5\t0.0\t4\t2 2 0 1"
## [168] "94\t4\t0.0\t4\t3 1"
## [169] "95\t7\t0.0\t4\t7"
## [170] "96\t3\t0.0\t4\t2 1"
## [171] "97\t2\t0.0\t4\t1 1"
## [172] "98\t3\t0.0\t4\t3"
## [173] "99\t3\t0.0\t4\t3"
## [174] "101\t1\t0.0\t4\t0 0 0 1"
## [175] "102\t1\t0.0\t4\t1"
## [176] "103\t1\t0.0\t4\t0 0 0 1"
## [177] "104\t1\t0.0\t4\t0 0 0 1"
## [178] "105\t3\t0.0\t4\t3"
## [179] "106\t7\t0.0\t4\t7"
## [180] "108\t3\t0.0\t4\t3"
## [181] "109\t1\t0.0\t4\t1"
## [182] "110\t1\t0.0\t4\t0 0 0 1"
## [183] "112\t2\t0.0\t4\t2"
## [184] "113\t2\t0.0\t4\t2"
## [185] "115\t1\t0.0\t4\t1"
## [186] "116\t1\t0.0\t4\t0 1"
## [187] "117\t3\t0.0\t4\t3"
## [188] "118\t2\t0.0\t4\t2"
## [189] "120\t2\t0.0\t4\t2"
## [190] "121\t4\t0.0\t4\t4"
## [191] "122\t1\t0.0\t4\t1"
## [192] "123\t1\t0.0\t4\t1"
## [193] "125\t2\t0.0\t4\t2"
## [194] "126\t1\t0.0\t4\t1"
## [195] "128\t1\t0.0\t4\t1"
## [196] "131\t3\t0.0\t4\t2 0 0 0 1"
## [197] "132\t1\t0.0\t4\t1"
## [198] "133\t1\t0.0\t4\t0 0 0 1"
## [199] "134\t3\t0.0\t4\t2 0 0 1"
## [200] "135\t1\t0.0\t4\t0 0 1"
## [201] "137\t2\t0.0\t4\t1 1"
## [202] "139\t1\t0.0\t4\t1"
## [203] "141\t1\t0.0\t4\t0 0 1"
## [204] "144\t1\t0.0\t4\t1"
## [205] "145\t1\t0.0\t4\t1"
## [206] "146\t1\t0.0\t4\t1"
## [207] "148\t2\t0.0\t4\t1 0 0 1"
## [208] "152\t1\t0.0\t4\t1"
## [209] "154\t1\t0.0\t4\t1"
## [210] "159\t1\t0.0\t4\t0 1"
## [211] "160\t2\t0.0\t4\t1 1"
## [212] "161\t1\t0.0\t4\t1"
## [213] "162\t1\t0.0\t4\t1"
## [214] "163\t1\t0.0\t4\t1"
## [215] "166\t1\t0.0\t4\t1"
## [216] "174\t1\t0.0\t4\t1"
## [217] "210\t1\t0.0\t4\t0 0 0 0 1"
##
## [[26]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14CRNA1_S26_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14CRNA1_S26_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14CRNA1_S26_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14CRNA1_S26_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.57 s (108 us/read; 0.56 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 5,310"
## [9] " Read 1 with adapter: 22 (0.4%)"
## [10] " Read 2 with adapter: 243 (4.6%)"
## [11] "Pairs written (passing filters): 5,310 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 2,230,200 bp"
## [14] " Read 1: 1,040,760 bp"
## [15] " Read 2: 1,189,440 bp"
## [16] "Total written (filtered): 2,211,302 bp (99.2%)"
## [17] " Read 1: 1,039,566 bp"
## [18] " Read 2: 1,171,736 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "7\t1\t0.3\t0\t1"
## [30] "31\t1\t0.0\t3\t1"
## [31] "33\t1\t0.0\t3\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 19 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 31.6%"
## [43] " C: 0.0%"
## [44] " G: 68.4%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "8\t1\t0.1\t0\t1"
## [51] "14\t1\t0.0\t1\t1"
## [52] "15\t1\t0.0\t1\t1"
## [53] "17\t1\t0.0\t1\t1"
## [54] "36\t1\t0.0\t2\t1"
## [55] "61\t5\t0.0\t2\t5"
## [56] "62\t1\t0.0\t2\t1"
## [57] "67\t1\t0.0\t2\t1"
## [58] "74\t3\t0.0\t2\t3"
## [59] "90\t3\t0.0\t2\t3"
## [60] "107\t1\t0.0\t2\t1"
## [61] ""
## [62] ""
## [63] "=== Second read: Adapter 3 ==="
## [64] ""
## [65] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 2 times"
## [66] ""
## [67] "No. of allowed errors:"
## [68] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [69] ""
## [70] "Overview of removed sequences"
## [71] "length\tcount\texpect\tmax.err\terror counts"
## [72] "12\t1\t0.0\t1\t0 1"
## [73] "125\t1\t0.0\t2\t1"
## [74] ""
## [75] ""
## [76] "=== Second read: Adapter 4 ==="
## [77] ""
## [78] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 241 times"
## [79] ""
## [80] "No. of allowed errors:"
## [81] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [82] ""
## [83] "Bases preceding removed adapters:"
## [84] " A: 22.4%"
## [85] " C: 10.4%"
## [86] " G: 67.2%"
## [87] " T: 0.0%"
## [88] " none/other: 0.0%"
## [89] ""
## [90] "Overview of removed sequences"
## [91] "length\tcount\texpect\tmax.err\terror counts"
## [92] "5\t1\t5.2\t0\t1"
## [93] "6\t5\t1.3\t0\t5"
## [94] "7\t2\t0.3\t0\t2"
## [95] "8\t3\t0.1\t0\t3"
## [96] "10\t1\t0.0\t1\t1"
## [97] "13\t2\t0.0\t1\t2"
## [98] "15\t2\t0.0\t1\t2"
## [99] "16\t4\t0.0\t1\t4"
## [100] "18\t1\t0.0\t1\t1"
## [101] "19\t2\t0.0\t1\t2"
## [102] "20\t2\t0.0\t2\t2"
## [103] "21\t1\t0.0\t2\t1"
## [104] "22\t2\t0.0\t2\t2"
## [105] "24\t2\t0.0\t2\t2"
## [106] "25\t2\t0.0\t2\t1 1"
## [107] "26\t4\t0.0\t2\t3 1"
## [108] "27\t1\t0.0\t2\t0 1"
## [109] "28\t2\t0.0\t2\t2"
## [110] "30\t1\t0.0\t3\t1"
## [111] "31\t3\t0.0\t3\t3"
## [112] "32\t1\t0.0\t3\t1"
## [113] "33\t2\t0.0\t3\t2"
## [114] "36\t1\t0.0\t3\t1"
## [115] "40\t1\t0.0\t4\t1"
## [116] "41\t3\t0.0\t4\t2 1"
## [117] "42\t2\t0.0\t4\t1 0 1"
## [118] "43\t4\t0.0\t4\t2 2"
## [119] "45\t5\t0.0\t4\t3 2"
## [120] "46\t2\t0.0\t4\t1 1"
## [121] "47\t1\t0.0\t4\t0 1"
## [122] "48\t1\t0.0\t4\t1"
## [123] "49\t4\t0.0\t4\t2 1 1"
## [124] "50\t3\t0.0\t4\t2 0 0 1"
## [125] "51\t3\t0.0\t4\t3"
## [126] "52\t1\t0.0\t4\t0 1"
## [127] "53\t1\t0.0\t4\t1"
## [128] "56\t2\t0.0\t4\t1 1"
## [129] "57\t6\t0.0\t4\t5 1"
## [130] "59\t1\t0.0\t4\t1"
## [131] "60\t2\t0.0\t4\t2"
## [132] "61\t3\t0.0\t4\t2 1"
## [133] "62\t4\t0.0\t4\t3 1"
## [134] "63\t7\t0.0\t4\t6 1"
## [135] "64\t1\t0.0\t4\t1"
## [136] "65\t3\t0.0\t4\t1 1 0 1"
## [137] "66\t2\t0.0\t4\t1 1"
## [138] "67\t5\t0.0\t4\t4 1"
## [139] "68\t4\t0.0\t4\t3 0 1"
## [140] "69\t1\t0.0\t4\t1"
## [141] "70\t1\t0.0\t4\t0 0 0 1"
## [142] "72\t1\t0.0\t4\t1"
## [143] "73\t3\t0.0\t4\t2 0 1"
## [144] "74\t1\t0.0\t4\t1"
## [145] "75\t1\t0.0\t4\t1"
## [146] "77\t3\t0.0\t4\t3"
## [147] "78\t1\t0.0\t4\t1"
## [148] "79\t3\t0.0\t4\t2 1"
## [149] "80\t3\t0.0\t4\t2 1"
## [150] "83\t3\t0.0\t4\t3"
## [151] "84\t5\t0.0\t4\t5"
## [152] "85\t12\t0.0\t4\t10 2"
## [153] "86\t3\t0.0\t4\t3"
## [154] "88\t2\t0.0\t4\t2"
## [155] "89\t6\t0.0\t4\t1 4 1"
## [156] "90\t2\t0.0\t4\t2"
## [157] "91\t2\t0.0\t4\t1 0 1"
## [158] "92\t2\t0.0\t4\t2"
## [159] "93\t1\t0.0\t4\t1"
## [160] "94\t1\t0.0\t4\t1"
## [161] "95\t2\t0.0\t4\t2"
## [162] "96\t2\t0.0\t4\t2"
## [163] "98\t1\t0.0\t4\t1"
## [164] "101\t3\t0.0\t4\t2 1"
## [165] "102\t5\t0.0\t4\t5"
## [166] "103\t4\t0.0\t4\t2 2"
## [167] "104\t3\t0.0\t4\t2 1"
## [168] "105\t1\t0.0\t4\t1"
## [169] "106\t1\t0.0\t4\t1"
## [170] "112\t2\t0.0\t4\t2"
## [171] "113\t1\t0.0\t4\t1"
## [172] "115\t3\t0.0\t4\t3"
## [173] "117\t2\t0.0\t4\t1 1"
## [174] "118\t3\t0.0\t4\t3"
## [175] "119\t5\t0.0\t4\t5"
## [176] "120\t3\t0.0\t4\t3"
## [177] "121\t1\t0.0\t4\t1"
## [178] "123\t2\t0.0\t4\t2"
## [179] "125\t2\t0.0\t4\t2"
## [180] "126\t1\t0.0\t4\t1"
## [181] "130\t1\t0.0\t4\t1"
## [182] "134\t1\t0.0\t4\t1"
## [183] "135\t1\t0.0\t4\t1"
## [184] "137\t1\t0.0\t4\t0 1"
## [185] "138\t1\t0.0\t4\t1"
## [186] "140\t2\t0.0\t4\t1 1"
## [187] "141\t1\t0.0\t4\t1"
## [188] "143\t2\t0.0\t4\t2"
## [189] "144\t2\t0.0\t4\t2"
## [190] "146\t1\t0.0\t4\t1"
## [191] "149\t1\t0.0\t4\t1"
## [192] "160\t1\t0.0\t4\t1"
## [193] "161\t1\t0.0\t4\t1"
## [194] "162\t2\t0.0\t4\t2"
## [195] "163\t1\t0.0\t4\t1"
##
## [[27]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14CRNA2_S27_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14CRNA2_S27_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14CRNA2_S27_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14CRNA2_S27_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.74 s (111 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 6,680"
## [9] " Read 1 with adapter: 186 (2.8%)"
## [10] " Read 2 with adapter: 1,031 (15.4%)"
## [11] "Pairs written (passing filters): 6,676 (99.9%)"
## [12] ""
## [13] "Total basepairs processed: 2,805,600 bp"
## [14] " Read 1: 1,309,280 bp"
## [15] " Read 2: 1,496,320 bp"
## [16] "Total written (filtered): 2,714,208 bp (96.7%)"
## [17] " Read 1: 1,297,036 bp"
## [18] " Read 2: 1,417,172 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 5 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "33\t2\t0.0\t3\t1 0 1"
## [30] "34\t2\t0.0\t3\t2"
## [31] "36\t1\t0.0\t3\t0 0 1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 181 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 84.5%"
## [43] " C: 0.6%"
## [44] " G: 13.3%"
## [45] " T: 1.7%"
## [46] " none/other: 0.0%"
## [47] "WARNING:"
## [48] " The adapter is preceded by \"A\" extremely often."
## [49] " The provided adapter sequence could be incomplete at its 3' end."
## [50] ""
## [51] "Overview of removed sequences"
## [52] "length\tcount\texpect\tmax.err\terror counts"
## [53] "5\t1\t6.5\t0\t1"
## [54] "7\t1\t0.4\t0\t1"
## [55] "15\t1\t0.0\t1\t1"
## [56] "26\t1\t0.0\t2\t1"
## [57] "28\t1\t0.0\t2\t1"
## [58] "29\t1\t0.0\t2\t1"
## [59] "30\t1\t0.0\t2\t1"
## [60] "33\t1\t0.0\t2\t1"
## [61] "36\t2\t0.0\t2\t2"
## [62] "54\t7\t0.0\t2\t7"
## [63] "55\t3\t0.0\t2\t3"
## [64] "59\t2\t0.0\t2\t1 1"
## [65] "60\t2\t0.0\t2\t2"
## [66] "61\t126\t0.0\t2\t122 4"
## [67] "62\t4\t0.0\t2\t4"
## [68] "63\t1\t0.0\t2\t1"
## [69] "67\t1\t0.0\t2\t0 1"
## [70] "69\t1\t0.0\t2\t1"
## [71] "71\t1\t0.0\t2\t1"
## [72] "74\t5\t0.0\t2\t5"
## [73] "82\t3\t0.0\t2\t3"
## [74] "90\t10\t0.0\t2\t10"
## [75] "91\t1\t0.0\t2\t1"
## [76] "96\t1\t0.0\t2\t1"
## [77] "99\t1\t0.0\t2\t0 1"
## [78] "123\t1\t0.0\t2\t1"
## [79] "135\t1\t0.0\t2\t1"
## [80] ""
## [81] ""
## [82] "=== Second read: Adapter 3 ==="
## [83] ""
## [84] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [85] ""
## [86] "No. of allowed errors:"
## [87] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [88] ""
## [89] "Overview of removed sequences"
## [90] "length\tcount\texpect\tmax.err\terror counts"
## [91] "16\t1\t0.0\t1\t0 1"
## [92] ""
## [93] ""
## [94] "=== Second read: Adapter 4 ==="
## [95] ""
## [96] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 1030 times"
## [97] ""
## [98] "No. of allowed errors:"
## [99] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [100] ""
## [101] "Bases preceding removed adapters:"
## [102] " A: 53.6%"
## [103] " C: 13.7%"
## [104] " G: 32.6%"
## [105] " T: 0.1%"
## [106] " none/other: 0.0%"
## [107] ""
## [108] "Overview of removed sequences"
## [109] "length\tcount\texpect\tmax.err\terror counts"
## [110] "5\t2\t6.5\t0\t2"
## [111] "6\t4\t1.6\t0\t4"
## [112] "7\t1\t0.4\t0\t1"
## [113] "8\t10\t0.1\t0\t10"
## [114] "9\t3\t0.0\t0\t3"
## [115] "10\t2\t0.0\t1\t2"
## [116] "11\t7\t0.0\t1\t6 1"
## [117] "12\t3\t0.0\t1\t3"
## [118] "13\t2\t0.0\t1\t1 1"
## [119] "14\t10\t0.0\t1\t7 3"
## [120] "15\t5\t0.0\t1\t4 1"
## [121] "16\t12\t0.0\t1\t11 1"
## [122] "18\t6\t0.0\t1\t5 1"
## [123] "19\t3\t0.0\t1\t3"
## [124] "20\t6\t0.0\t2\t4 2"
## [125] "21\t1\t0.0\t2\t1"
## [126] "22\t9\t0.0\t2\t7 0 2"
## [127] "23\t6\t0.0\t2\t3 2 1"
## [128] "24\t5\t0.0\t2\t3 2"
## [129] "25\t4\t0.0\t2\t1 3"
## [130] "26\t6\t0.0\t2\t4 2"
## [131] "27\t7\t0.0\t2\t4 2 1"
## [132] "28\t3\t0.0\t2\t1 2"
## [133] "29\t4\t0.0\t2\t3 0 1"
## [134] "30\t6\t0.0\t3\t1 5"
## [135] "31\t7\t0.0\t3\t2 4 1"
## [136] "32\t5\t0.0\t3\t3 2"
## [137] "33\t5\t0.0\t3\t3 2"
## [138] "34\t3\t0.0\t3\t2 1"
## [139] "35\t12\t0.0\t3\t9 2 1"
## [140] "36\t7\t0.0\t3\t6 1"
## [141] "38\t4\t0.0\t3\t2 2"
## [142] "39\t8\t0.0\t3\t4 2 1 1"
## [143] "40\t7\t0.0\t4\t4 3"
## [144] "41\t10\t0.0\t4\t3 6 1"
## [145] "42\t6\t0.0\t4\t2 4"
## [146] "43\t9\t0.0\t4\t7 1 0 1"
## [147] "44\t4\t0.0\t4\t3 1"
## [148] "45\t16\t0.0\t4\t12 3 0 1"
## [149] "46\t13\t0.0\t4\t8 5"
## [150] "47\t6\t0.0\t4\t4 1 1"
## [151] "48\t3\t0.0\t4\t1 2"
## [152] "49\t6\t0.0\t4\t3 1 2"
## [153] "50\t7\t0.0\t4\t5 1 1"
## [154] "51\t11\t0.0\t4\t8 3"
## [155] "52\t15\t0.0\t4\t6 9"
## [156] "53\t4\t0.0\t4\t2 1 1"
## [157] "54\t5\t0.0\t4\t3 1 1"
## [158] "55\t1\t0.0\t4\t1"
## [159] "56\t9\t0.0\t4\t5 2 1 1"
## [160] "57\t9\t0.0\t4\t7 1 1"
## [161] "58\t9\t0.0\t4\t6 2 0 0 1"
## [162] "59\t6\t0.0\t4\t2 4"
## [163] "60\t20\t0.0\t4\t17 2 0 1"
## [164] "61\t4\t0.0\t4\t2 2"
## [165] "62\t8\t0.0\t4\t4 3 1"
## [166] "63\t13\t0.0\t4\t11 2"
## [167] "64\t16\t0.0\t4\t13 1 2"
## [168] "65\t10\t0.0\t4\t7 3"
## [169] "66\t5\t0.0\t4\t4 1"
## [170] "67\t5\t0.0\t4\t5"
## [171] "68\t4\t0.0\t4\t4"
## [172] "69\t9\t0.0\t4\t8 1"
## [173] "70\t9\t0.0\t4\t6 3"
## [174] "71\t4\t0.0\t4\t2 2"
## [175] "72\t3\t0.0\t4\t3"
## [176] "73\t2\t0.0\t4\t1 1"
## [177] "74\t4\t0.0\t4\t3 1"
## [178] "75\t5\t0.0\t4\t5"
## [179] "76\t3\t0.0\t4\t1 2"
## [180] "77\t9\t0.0\t4\t6 3"
## [181] "78\t7\t0.0\t4\t4 3"
## [182] "79\t16\t0.0\t4\t9 7"
## [183] "80\t3\t0.0\t4\t3"
## [184] "81\t3\t0.0\t4\t3"
## [185] "82\t8\t0.0\t4\t0 5 2 1"
## [186] "83\t11\t0.0\t4\t7 4"
## [187] "84\t18\t0.0\t4\t14 4"
## [188] "85\t24\t0.0\t4\t17 6 1"
## [189] "86\t15\t0.0\t4\t10 5"
## [190] "87\t7\t0.0\t4\t3 2 2"
## [191] "88\t7\t0.0\t4\t2 3 2"
## [192] "89\t135\t0.0\t4\t9 102 24"
## [193] "90\t2\t0.0\t4\t0 2"
## [194] "91\t9\t0.0\t4\t5 4"
## [195] "92\t12\t0.0\t4\t10 2"
## [196] "93\t6\t0.0\t4\t5 1"
## [197] "94\t17\t0.0\t4\t13 4"
## [198] "95\t11\t0.0\t4\t8 2 0 1"
## [199] "96\t5\t0.0\t4\t5"
## [200] "97\t6\t0.0\t4\t3 2 0 1"
## [201] "98\t3\t0.0\t4\t2 1"
## [202] "99\t3\t0.0\t4\t3"
## [203] "100\t7\t0.0\t4\t5 2"
## [204] "101\t1\t0.0\t4\t0 1"
## [205] "102\t10\t0.0\t4\t10"
## [206] "103\t7\t0.0\t4\t4 3"
## [207] "104\t11\t0.0\t4\t10 1"
## [208] "105\t3\t0.0\t4\t2 1"
## [209] "106\t1\t0.0\t4\t1"
## [210] "108\t4\t0.0\t4\t1 3"
## [211] "109\t3\t0.0\t4\t3"
## [212] "110\t5\t0.0\t4\t2 3"
## [213] "111\t3\t0.0\t4\t1 2"
## [214] "112\t12\t0.0\t4\t7 4 0 0 1"
## [215] "113\t5\t0.0\t4\t3 1 1"
## [216] "114\t4\t0.0\t4\t2 2"
## [217] "115\t4\t0.0\t4\t3 1"
## [218] "116\t8\t0.0\t4\t6 1 1"
## [219] "117\t7\t0.0\t4\t4 3"
## [220] "118\t13\t0.0\t4\t4 8 1"
## [221] "119\t14\t0.0\t4\t10 4"
## [222] "120\t6\t0.0\t4\t5 1"
## [223] "121\t2\t0.0\t4\t2"
## [224] "123\t2\t0.0\t4\t2"
## [225] "124\t5\t0.0\t4\t4 0 0 1"
## [226] "125\t2\t0.0\t4\t2"
## [227] "126\t6\t0.0\t4\t4 1 1"
## [228] "127\t4\t0.0\t4\t1 2 0 1"
## [229] "128\t2\t0.0\t4\t1 1"
## [230] "129\t3\t0.0\t4\t2 1"
## [231] "130\t1\t0.0\t4\t1"
## [232] "131\t2\t0.0\t4\t1 1"
## [233] "132\t5\t0.0\t4\t2 3"
## [234] "133\t1\t0.0\t4\t1"
## [235] "134\t1\t0.0\t4\t0 1"
## [236] "135\t1\t0.0\t4\t0 1"
## [237] "136\t3\t0.0\t4\t2 0 1"
## [238] "137\t2\t0.0\t4\t1 1"
## [239] "138\t7\t0.0\t4\t5 2"
## [240] "139\t4\t0.0\t4\t4"
## [241] "140\t7\t0.0\t4\t6 0 0 0 1"
## [242] "141\t2\t0.0\t4\t1 1"
## [243] "142\t4\t0.0\t4\t4"
## [244] "144\t1\t0.0\t4\t1"
## [245] "145\t1\t0.0\t4\t0 1"
## [246] "146\t2\t0.0\t4\t1 1"
## [247] "147\t1\t0.0\t4\t1"
## [248] "148\t3\t0.0\t4\t2 1"
## [249] "149\t4\t0.0\t4\t4"
## [250] "150\t1\t0.0\t4\t0 1"
## [251] "151\t2\t0.0\t4\t1 1"
## [252] "152\t3\t0.0\t4\t3"
## [253] "153\t1\t0.0\t4\t1"
## [254] "154\t1\t0.0\t4\t1"
## [255] "158\t2\t0.0\t4\t2"
## [256] "159\t4\t0.0\t4\t4"
## [257] "160\t3\t0.0\t4\t2 1"
## [258] "161\t1\t0.0\t4\t0 1"
## [259] "162\t2\t0.0\t4\t2"
## [260] "163\t1\t0.0\t4\t0 1"
## [261] "165\t1\t0.0\t4\t1"
## [262] "169\t2\t0.0\t4\t1 1"
## [263] "171\t1\t0.0\t4\t1"
## [264] "180\t3\t0.0\t4\t3"
## [265] "188\t1\t0.0\t4\t1"
## [266] ""
## [267] ""
## [268] "WARNING:"
## [269] " One or more of your adapter sequences may be incomplete."
## [270] " Please see the detailed output above."
##
## [[28]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/14CRNA3_S28_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/14CRNA3_S28_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/14CRNA3_S28_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/14CRNA3_S28_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.51 s (108 us/read; 0.55 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 4,749"
## [9] " Read 1 with adapter: 34 (0.7%)"
## [10] " Read 2 with adapter: 369 (7.8%)"
## [11] "Pairs written (passing filters): 4,749 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 1,994,580 bp"
## [14] " Read 1: 930,804 bp"
## [15] " Read 2: 1,063,776 bp"
## [16] "Total written (filtered): 1,965,785 bp (98.6%)"
## [17] " Read 1: 929,307 bp"
## [18] " Read 2: 1,036,478 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 15 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "10\t1\t0.0\t1\t1"
## [30] "11\t1\t0.0\t1\t1"
## [31] "15\t1\t0.0\t1\t0 1"
## [32] "17\t6\t0.0\t1\t6"
## [33] "20\t1\t0.0\t2\t1"
## [34] "30\t1\t0.0\t3\t0 1"
## [35] "31\t4\t0.0\t3\t4"
## [36] ""
## [37] ""
## [38] "=== First read: Adapter 2 ==="
## [39] ""
## [40] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 19 times"
## [41] ""
## [42] "No. of allowed errors:"
## [43] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [44] ""
## [45] "Bases preceding removed adapters:"
## [46] " A: 52.6%"
## [47] " C: 0.0%"
## [48] " G: 42.1%"
## [49] " T: 5.3%"
## [50] " none/other: 0.0%"
## [51] ""
## [52] "Overview of removed sequences"
## [53] "length\tcount\texpect\tmax.err\terror counts"
## [54] "12\t1\t0.0\t1\t1"
## [55] "21\t1\t0.0\t2\t1"
## [56] "36\t1\t0.0\t2\t1"
## [57] "61\t9\t0.0\t2\t8 1"
## [58] "74\t3\t0.0\t2\t3"
## [59] "82\t2\t0.0\t2\t2"
## [60] "90\t1\t0.0\t2\t1"
## [61] "91\t1\t0.0\t2\t1"
## [62] ""
## [63] ""
## [64] "=== Second read: Adapter 3 ==="
## [65] ""
## [66] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [67] ""
## [68] "=== Second read: Adapter 4 ==="
## [69] ""
## [70] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 369 times"
## [71] ""
## [72] "No. of allowed errors:"
## [73] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [74] ""
## [75] "Bases preceding removed adapters:"
## [76] " A: 21.4%"
## [77] " C: 7.6%"
## [78] " G: 71.0%"
## [79] " T: 0.0%"
## [80] " none/other: 0.0%"
## [81] ""
## [82] "Overview of removed sequences"
## [83] "length\tcount\texpect\tmax.err\terror counts"
## [84] "5\t3\t4.6\t0\t3"
## [85] "6\t2\t1.2\t0\t2"
## [86] "7\t3\t0.3\t0\t3"
## [87] "8\t3\t0.1\t0\t3"
## [88] "9\t2\t0.0\t0\t2"
## [89] "11\t1\t0.0\t1\t1"
## [90] "12\t3\t0.0\t1\t1 2"
## [91] "13\t2\t0.0\t1\t2"
## [92] "14\t1\t0.0\t1\t1"
## [93] "15\t3\t0.0\t1\t3"
## [94] "16\t1\t0.0\t1\t1"
## [95] "17\t1\t0.0\t1\t0 1"
## [96] "18\t1\t0.0\t1\t1"
## [97] "19\t1\t0.0\t1\t1"
## [98] "20\t3\t0.0\t2\t3"
## [99] "21\t4\t0.0\t2\t4"
## [100] "22\t3\t0.0\t2\t3"
## [101] "23\t3\t0.0\t2\t3"
## [102] "24\t3\t0.0\t2\t2 1"
## [103] "25\t3\t0.0\t2\t2 1"
## [104] "26\t2\t0.0\t2\t1 0 1"
## [105] "27\t1\t0.0\t2\t0 1"
## [106] "30\t2\t0.0\t3\t1 1"
## [107] "31\t6\t0.0\t3\t5 1"
## [108] "32\t2\t0.0\t3\t1 1"
## [109] "33\t5\t0.0\t3\t3 2"
## [110] "34\t2\t0.0\t3\t2"
## [111] "35\t6\t0.0\t3\t4 2"
## [112] "36\t3\t0.0\t3\t2 0 0 1"
## [113] "37\t2\t0.0\t3\t1 0 1"
## [114] "38\t1\t0.0\t3\t1"
## [115] "39\t1\t0.0\t3\t1"
## [116] "40\t5\t0.0\t4\t3 1 0 1"
## [117] "42\t1\t0.0\t4\t1"
## [118] "43\t3\t0.0\t4\t3"
## [119] "44\t5\t0.0\t4\t3 1 1"
## [120] "45\t3\t0.0\t4\t3"
## [121] "46\t2\t0.0\t4\t1 1"
## [122] "47\t4\t0.0\t4\t3 0 0 1"
## [123] "49\t3\t0.0\t4\t3"
## [124] "50\t7\t0.0\t4\t5 1 1"
## [125] "51\t8\t0.0\t4\t6 1 1"
## [126] "52\t2\t0.0\t4\t2"
## [127] "53\t3\t0.0\t4\t2 1"
## [128] "54\t2\t0.0\t4\t2"
## [129] "55\t3\t0.0\t4\t3"
## [130] "56\t4\t0.0\t4\t2 2"
## [131] "57\t2\t0.0\t4\t0 1 1"
## [132] "59\t3\t0.0\t4\t3"
## [133] "60\t8\t0.0\t4\t6 1 0 0 1"
## [134] "61\t1\t0.0\t4\t1"
## [135] "62\t3\t0.0\t4\t2 0 1"
## [136] "63\t7\t0.0\t4\t5 2"
## [137] "64\t7\t0.0\t4\t6 1"
## [138] "65\t5\t0.0\t4\t5"
## [139] "66\t3\t0.0\t4\t3"
## [140] "67\t2\t0.0\t4\t1 1"
## [141] "69\t4\t0.0\t4\t3 1"
## [142] "70\t2\t0.0\t4\t2"
## [143] "71\t1\t0.0\t4\t1"
## [144] "72\t1\t0.0\t4\t0 1"
## [145] "73\t1\t0.0\t4\t1"
## [146] "74\t1\t0.0\t4\t0 1"
## [147] "75\t4\t0.0\t4\t4"
## [148] "76\t3\t0.0\t4\t2 1"
## [149] "77\t7\t0.0\t4\t5 1 1"
## [150] "79\t3\t0.0\t4\t2 1"
## [151] "80\t1\t0.0\t4\t1"
## [152] "81\t4\t0.0\t4\t4"
## [153] "82\t1\t0.0\t4\t1"
## [154] "83\t8\t0.0\t4\t8"
## [155] "84\t6\t0.0\t4\t6"
## [156] "85\t11\t0.0\t4\t10 1"
## [157] "86\t4\t0.0\t4\t3 1"
## [158] "87\t2\t0.0\t4\t2"
## [159] "88\t1\t0.0\t4\t1"
## [160] "89\t9\t0.0\t4\t2 6 1"
## [161] "90\t3\t0.0\t4\t3"
## [162] "91\t1\t0.0\t4\t1"
## [163] "92\t4\t0.0\t4\t3 1"
## [164] "93\t3\t0.0\t4\t3"
## [165] "94\t3\t0.0\t4\t2 1"
## [166] "95\t3\t0.0\t4\t3"
## [167] "96\t3\t0.0\t4\t3"
## [168] "97\t3\t0.0\t4\t2 0 0 1"
## [169] "98\t1\t0.0\t4\t1"
## [170] "100\t1\t0.0\t4\t1"
## [171] "101\t1\t0.0\t4\t1"
## [172] "102\t6\t0.0\t4\t4 2"
## [173] "103\t7\t0.0\t4\t7"
## [174] "104\t7\t0.0\t4\t5 2"
## [175] "105\t1\t0.0\t4\t1"
## [176] "106\t1\t0.0\t4\t1"
## [177] "108\t1\t0.0\t4\t1"
## [178] "109\t2\t0.0\t4\t2"
## [179] "110\t3\t0.0\t4\t2 1"
## [180] "112\t1\t0.0\t4\t1"
## [181] "113\t2\t0.0\t4\t2"
## [182] "115\t2\t0.0\t4\t2"
## [183] "116\t4\t0.0\t4\t4"
## [184] "117\t4\t0.0\t4\t4"
## [185] "118\t3\t0.0\t4\t3"
## [186] "119\t2\t0.0\t4\t2"
## [187] "120\t2\t0.0\t4\t2"
## [188] "121\t3\t0.0\t4\t2 1"
## [189] "122\t2\t0.0\t4\t2"
## [190] "123\t1\t0.0\t4\t1"
## [191] "124\t3\t0.0\t4\t3"
## [192] "125\t1\t0.0\t4\t1"
## [193] "126\t1\t0.0\t4\t1"
## [194] "131\t1\t0.0\t4\t1"
## [195] "133\t1\t0.0\t4\t1"
## [196] "135\t1\t0.0\t4\t1"
## [197] "138\t1\t0.0\t4\t1"
## [198] "139\t4\t0.0\t4\t4"
## [199] "140\t5\t0.0\t4\t4 1"
## [200] "141\t2\t0.0\t4\t2"
## [201] "143\t2\t0.0\t4\t2"
## [202] "144\t2\t0.0\t4\t1 1"
## [203] "145\t2\t0.0\t4\t1 1"
## [204] "148\t1\t0.0\t4\t1"
## [205] "150\t1\t0.0\t4\t1"
## [206] "152\t3\t0.0\t4\t3"
## [207] "160\t2\t0.0\t4\t2"
## [208] "162\t1\t0.0\t4\t1"
## [209] "163\t2\t0.0\t4\t2"
## [210] "165\t1\t0.0\t4\t1"
## [211] "170\t1\t0.0\t4\t1"
## [212] "173\t2\t0.0\t4\t2"
##
## [[29]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1881_S29_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1881_S29_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1881_S29_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1881_S29_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.86 s (124 us/read; 0.49 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 6,964"
## [9] " Read 1 with adapter: 25 (0.4%)"
## [10] " Read 2 with adapter: 346 (5.0%)"
## [11] "Pairs written (passing filters): 6,964 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 2,924,880 bp"
## [14] " Read 1: 1,364,944 bp"
## [15] " Read 2: 1,559,936 bp"
## [16] "Total written (filtered): 2,902,335 bp (99.2%)"
## [17] " Read 1: 1,364,349 bp"
## [18] " Read 2: 1,537,986 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 19 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t6.8\t0\t1"
## [30] "6\t2\t1.7\t0\t2"
## [31] "12\t1\t0.0\t1\t1"
## [32] "16\t1\t0.0\t1\t1"
## [33] "17\t7\t0.0\t1\t7"
## [34] "25\t1\t0.0\t2\t1"
## [35] "31\t5\t0.0\t3\t4 1"
## [36] "56\t1\t0.0\t4\t1"
## [37] ""
## [38] ""
## [39] "=== First read: Adapter 2 ==="
## [40] ""
## [41] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 6 times"
## [42] ""
## [43] "No. of allowed errors:"
## [44] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [45] ""
## [46] "Bases preceding removed adapters:"
## [47] " A: 33.3%"
## [48] " C: 0.0%"
## [49] " G: 50.0%"
## [50] " T: 16.7%"
## [51] " none/other: 0.0%"
## [52] ""
## [53] "Overview of removed sequences"
## [54] "length\tcount\texpect\tmax.err\terror counts"
## [55] "6\t1\t1.7\t0\t1"
## [56] "10\t2\t0.0\t1\t2"
## [57] "19\t1\t0.0\t1\t1"
## [58] "30\t1\t0.0\t2\t1"
## [59] "120\t1\t0.0\t2\t1"
## [60] ""
## [61] ""
## [62] "=== Second read: Adapter 3 ==="
## [63] ""
## [64] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 3 times"
## [65] ""
## [66] "No. of allowed errors:"
## [67] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [68] ""
## [69] "Overview of removed sequences"
## [70] "length\tcount\texpect\tmax.err\terror counts"
## [71] "6\t1\t1.7\t0\t1"
## [72] "16\t2\t0.0\t1\t2"
## [73] ""
## [74] ""
## [75] "=== Second read: Adapter 4 ==="
## [76] ""
## [77] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 343 times"
## [78] ""
## [79] "No. of allowed errors:"
## [80] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [81] ""
## [82] "Bases preceding removed adapters:"
## [83] " A: 65.0%"
## [84] " C: 28.0%"
## [85] " G: 3.8%"
## [86] " T: 3.2%"
## [87] " none/other: 0.0%"
## [88] ""
## [89] "Overview of removed sequences"
## [90] "length\tcount\texpect\tmax.err\terror counts"
## [91] "5\t4\t6.8\t0\t4"
## [92] "6\t2\t1.7\t0\t2"
## [93] "7\t2\t0.4\t0\t2"
## [94] "8\t3\t0.1\t0\t3"
## [95] "9\t4\t0.0\t0\t4"
## [96] "11\t1\t0.0\t1\t1"
## [97] "12\t2\t0.0\t1\t2"
## [98] "13\t9\t0.0\t1\t9"
## [99] "14\t9\t0.0\t1\t8 1"
## [100] "15\t8\t0.0\t1\t5 3"
## [101] "16\t8\t0.0\t1\t6 2"
## [102] "17\t7\t0.0\t1\t7"
## [103] "18\t1\t0.0\t1\t1"
## [104] "20\t7\t0.0\t2\t5 1 1"
## [105] "21\t3\t0.0\t2\t3"
## [106] "22\t2\t0.0\t2\t2"
## [107] "23\t3\t0.0\t2\t2 1"
## [108] "24\t4\t0.0\t2\t4"
## [109] "25\t1\t0.0\t2\t1"
## [110] "26\t1\t0.0\t2\t1"
## [111] "27\t5\t0.0\t2\t3 2"
## [112] "28\t1\t0.0\t2\t1"
## [113] "29\t1\t0.0\t2\t1"
## [114] "30\t4\t0.0\t3\t2 1 1"
## [115] "31\t1\t0.0\t3\t1"
## [116] "33\t1\t0.0\t3\t0 1"
## [117] "34\t2\t0.0\t3\t1 1"
## [118] "35\t4\t0.0\t3\t2 1 1"
## [119] "36\t2\t0.0\t3\t1 0 1"
## [120] "37\t1\t0.0\t3\t1"
## [121] "38\t4\t0.0\t3\t4"
## [122] "39\t2\t0.0\t3\t2"
## [123] "40\t2\t0.0\t4\t1 1"
## [124] "41\t4\t0.0\t4\t4"
## [125] "42\t3\t0.0\t4\t2 1"
## [126] "43\t4\t0.0\t4\t4"
## [127] "44\t2\t0.0\t4\t1 0 1"
## [128] "45\t5\t0.0\t4\t3 1 0 1"
## [129] "46\t5\t0.0\t4\t4 1"
## [130] "47\t2\t0.0\t4\t1 1"
## [131] "48\t2\t0.0\t4\t1 1"
## [132] "49\t3\t0.0\t4\t3"
## [133] "51\t4\t0.0\t4\t2 1 1"
## [134] "52\t5\t0.0\t4\t2 2 1"
## [135] "53\t4\t0.0\t4\t1 3"
## [136] "54\t1\t0.0\t4\t0 1"
## [137] "55\t2\t0.0\t4\t2"
## [138] "56\t3\t0.0\t4\t1 2"
## [139] "57\t2\t0.0\t4\t2"
## [140] "58\t6\t0.0\t4\t5 0 1"
## [141] "59\t1\t0.0\t4\t0 1"
## [142] "60\t1\t0.0\t4\t1"
## [143] "61\t1\t0.0\t4\t0 0 0 0 1"
## [144] "63\t5\t0.0\t4\t5"
## [145] "64\t6\t0.0\t4\t6"
## [146] "65\t5\t0.0\t4\t5"
## [147] "66\t5\t0.0\t4\t3 1 1"
## [148] "67\t3\t0.0\t4\t3"
## [149] "69\t1\t0.0\t4\t1"
## [150] "70\t1\t0.0\t4\t1"
## [151] "71\t2\t0.0\t4\t2"
## [152] "72\t3\t0.0\t4\t3"
## [153] "73\t3\t0.0\t4\t3"
## [154] "74\t4\t0.0\t4\t4"
## [155] "75\t4\t0.0\t4\t4"
## [156] "76\t2\t0.0\t4\t2"
## [157] "77\t1\t0.0\t4\t1"
## [158] "78\t3\t0.0\t4\t2 1"
## [159] "79\t5\t0.0\t4\t5"
## [160] "81\t2\t0.0\t4\t2"
## [161] "82\t2\t0.0\t4\t2"
## [162] "84\t3\t0.0\t4\t3"
## [163] "85\t7\t0.0\t4\t7"
## [164] "86\t8\t0.0\t4\t6 1 1"
## [165] "87\t1\t0.0\t4\t1"
## [166] "88\t3\t0.0\t4\t1 0 0 2"
## [167] "89\t1\t0.0\t4\t1"
## [168] "91\t1\t0.0\t4\t1"
## [169] "92\t2\t0.0\t4\t2"
## [170] "93\t5\t0.0\t4\t5"
## [171] "94\t5\t0.0\t4\t5"
## [172] "95\t3\t0.0\t4\t2 0 0 1"
## [173] "96\t3\t0.0\t4\t3"
## [174] "97\t1\t0.0\t4\t1"
## [175] "98\t5\t0.0\t4\t4 1"
## [176] "99\t1\t0.0\t4\t1"
## [177] "101\t2\t0.0\t4\t2"
## [178] "104\t7\t0.0\t4\t7"
## [179] "105\t3\t0.0\t4\t3"
## [180] "106\t4\t0.0\t4\t3 0 0 0 1"
## [181] "107\t2\t0.0\t4\t1 1"
## [182] "110\t1\t0.0\t4\t1"
## [183] "111\t1\t0.0\t4\t1"
## [184] "112\t1\t0.0\t4\t1"
## [185] "114\t2\t0.0\t4\t1 1"
## [186] "116\t3\t0.0\t4\t3"
## [187] "117\t3\t0.0\t4\t2 1"
## [188] "118\t1\t0.0\t4\t1"
## [189] "119\t2\t0.0\t4\t1 0 0 1"
## [190] "120\t1\t0.0\t4\t1"
## [191] "121\t5\t0.0\t4\t3 2"
## [192] "122\t1\t0.0\t4\t1"
## [193] "123\t1\t0.0\t4\t1"
## [194] "125\t3\t0.0\t4\t3"
## [195] "128\t1\t0.0\t4\t1"
## [196] "129\t1\t0.0\t4\t1"
## [197] "133\t1\t0.0\t4\t1"
## [198] "135\t2\t0.0\t4\t2"
## [199] "136\t1\t0.0\t4\t1"
## [200] "138\t1\t0.0\t4\t1"
## [201] "139\t3\t0.0\t4\t2 0 0 1"
## [202] "140\t1\t0.0\t4\t1"
## [203] "141\t1\t0.0\t4\t1"
## [204] "142\t1\t0.0\t4\t1"
## [205] "146\t1\t0.0\t4\t1"
## [206] "147\t1\t0.0\t4\t1"
## [207] "148\t1\t0.0\t4\t1"
## [208] "149\t1\t0.0\t4\t1"
## [209] "158\t1\t0.0\t4\t1"
## [210] "160\t3\t0.0\t4\t3"
## [211] "172\t2\t0.0\t4\t1 1"
##
## [[30]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1882_S30_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1882_S30_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1882_S30_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1882_S30_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.74 s (125 us/read; 0.48 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 5,922"
## [9] " Read 1 with adapter: 44 (0.7%)"
## [10] " Read 2 with adapter: 282 (4.8%)"
## [11] "Pairs written (passing filters): 5,921 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 2,487,240 bp"
## [14] " Read 1: 1,160,712 bp"
## [15] " Read 2: 1,326,528 bp"
## [16] "Total written (filtered): 2,468,571 bp (99.2%)"
## [17] " Read 1: 1,159,473 bp"
## [18] " Read 2: 1,309,098 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 28 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "6\t1\t1.4\t0\t1"
## [30] "14\t1\t0.0\t1\t0 1"
## [31] "17\t19\t0.0\t1\t18 1"
## [32] "21\t1\t0.0\t2\t1"
## [33] "30\t1\t0.0\t3\t1"
## [34] "31\t4\t0.0\t3\t4"
## [35] "60\t1\t0.0\t4\t0 1"
## [36] ""
## [37] ""
## [38] "=== First read: Adapter 2 ==="
## [39] ""
## [40] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 16 times"
## [41] ""
## [42] "No. of allowed errors:"
## [43] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [44] ""
## [45] "Bases preceding removed adapters:"
## [46] " A: 25.0%"
## [47] " C: 43.8%"
## [48] " G: 25.0%"
## [49] " T: 6.2%"
## [50] " none/other: 0.0%"
## [51] ""
## [52] "Overview of removed sequences"
## [53] "length\tcount\texpect\tmax.err\terror counts"
## [54] "6\t1\t1.4\t0\t1"
## [55] "7\t1\t0.4\t0\t1"
## [56] "13\t7\t0.0\t1\t7"
## [57] "29\t1\t0.0\t2\t1"
## [58] "38\t1\t0.0\t2\t1"
## [59] "39\t1\t0.0\t2\t1"
## [60] "75\t2\t0.0\t2\t2"
## [61] "78\t1\t0.0\t2\t1"
## [62] "87\t1\t0.0\t2\t1"
## [63] ""
## [64] ""
## [65] "=== Second read: Adapter 3 ==="
## [66] ""
## [67] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [68] ""
## [69] "No. of allowed errors:"
## [70] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [71] ""
## [72] "Overview of removed sequences"
## [73] "length\tcount\texpect\tmax.err\terror counts"
## [74] "25\t1\t0.0\t2\t0 1"
## [75] ""
## [76] ""
## [77] "=== Second read: Adapter 4 ==="
## [78] ""
## [79] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 281 times"
## [80] ""
## [81] "No. of allowed errors:"
## [82] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [83] ""
## [84] "Bases preceding removed adapters:"
## [85] " A: 60.9%"
## [86] " C: 29.9%"
## [87] " G: 5.7%"
## [88] " T: 3.6%"
## [89] " none/other: 0.0%"
## [90] ""
## [91] "Overview of removed sequences"
## [92] "length\tcount\texpect\tmax.err\terror counts"
## [93] "5\t6\t5.8\t0\t6"
## [94] "6\t5\t1.4\t0\t5"
## [95] "8\t3\t0.1\t0\t3"
## [96] "9\t1\t0.0\t0\t1"
## [97] "10\t1\t0.0\t1\t0 1"
## [98] "12\t2\t0.0\t1\t2"
## [99] "13\t8\t0.0\t1\t7 1"
## [100] "14\t6\t0.0\t1\t5 1"
## [101] "15\t5\t0.0\t1\t5"
## [102] "16\t4\t0.0\t1\t4"
## [103] "17\t4\t0.0\t1\t4"
## [104] "18\t1\t0.0\t1\t1"
## [105] "19\t1\t0.0\t1\t1"
## [106] "20\t1\t0.0\t2\t1"
## [107] "21\t1\t0.0\t2\t1"
## [108] "22\t4\t0.0\t2\t4"
## [109] "23\t9\t0.0\t2\t8 1"
## [110] "24\t1\t0.0\t2\t1"
## [111] "25\t3\t0.0\t2\t2 1"
## [112] "26\t2\t0.0\t2\t2"
## [113] "27\t3\t0.0\t2\t3"
## [114] "28\t4\t0.0\t2\t3 1"
## [115] "31\t3\t0.0\t3\t2 1"
## [116] "32\t1\t0.0\t3\t0 1"
## [117] "33\t5\t0.0\t3\t3 1 1"
## [118] "34\t2\t0.0\t3\t2"
## [119] "35\t4\t0.0\t3\t3 1"
## [120] "36\t1\t0.0\t3\t1"
## [121] "37\t2\t0.0\t3\t2"
## [122] "38\t1\t0.0\t3\t1"
## [123] "39\t1\t0.0\t3\t1"
## [124] "40\t1\t0.0\t4\t1"
## [125] "41\t10\t0.0\t4\t9 0 1"
## [126] "42\t5\t0.0\t4\t4 0 0 1"
## [127] "43\t3\t0.0\t4\t2 0 0 1"
## [128] "44\t1\t0.0\t4\t1"
## [129] "45\t2\t0.0\t4\t2"
## [130] "46\t3\t0.0\t4\t3"
## [131] "47\t3\t0.0\t4\t3"
## [132] "48\t2\t0.0\t4\t2"
## [133] "50\t1\t0.0\t4\t1"
## [134] "51\t1\t0.0\t4\t1"
## [135] "52\t2\t0.0\t4\t1 0 1"
## [136] "53\t2\t0.0\t4\t2"
## [137] "54\t5\t0.0\t4\t4 0 1"
## [138] "55\t5\t0.0\t4\t5"
## [139] "56\t3\t0.0\t4\t3"
## [140] "57\t3\t0.0\t4\t3"
## [141] "58\t2\t0.0\t4\t2"
## [142] "59\t2\t0.0\t4\t2"
## [143] "60\t1\t0.0\t4\t1"
## [144] "61\t1\t0.0\t4\t1"
## [145] "62\t1\t0.0\t4\t0 1"
## [146] "63\t3\t0.0\t4\t3"
## [147] "64\t1\t0.0\t4\t1"
## [148] "65\t3\t0.0\t4\t3"
## [149] "66\t3\t0.0\t4\t3"
## [150] "67\t9\t0.0\t4\t9"
## [151] "69\t1\t0.0\t4\t1"
## [152] "70\t1\t0.0\t4\t1"
## [153] "71\t3\t0.0\t4\t3"
## [154] "72\t1\t0.0\t4\t1"
## [155] "73\t2\t0.0\t4\t2"
## [156] "74\t1\t0.0\t4\t1"
## [157] "75\t3\t0.0\t4\t3"
## [158] "77\t3\t0.0\t4\t2 1"
## [159] "78\t1\t0.0\t4\t0 1"
## [160] "79\t1\t0.0\t4\t1"
## [161] "80\t1\t0.0\t4\t1"
## [162] "81\t1\t0.0\t4\t1"
## [163] "82\t2\t0.0\t4\t2"
## [164] "83\t2\t0.0\t4\t2"
## [165] "84\t3\t0.0\t4\t3"
## [166] "85\t7\t0.0\t4\t6 1"
## [167] "86\t2\t0.0\t4\t2"
## [168] "87\t1\t0.0\t4\t1"
## [169] "88\t1\t0.0\t4\t0 1"
## [170] "89\t1\t0.0\t4\t0 1"
## [171] "92\t1\t0.0\t4\t1"
## [172] "93\t1\t0.0\t4\t1"
## [173] "94\t5\t0.0\t4\t5"
## [174] "95\t2\t0.0\t4\t2"
## [175] "96\t3\t0.0\t4\t2 1"
## [176] "98\t3\t0.0\t4\t2 0 0 1"
## [177] "103\t6\t0.0\t4\t6"
## [178] "104\t6\t0.0\t4\t5 1"
## [179] "105\t1\t0.0\t4\t1"
## [180] "106\t5\t0.0\t4\t4 0 0 1"
## [181] "108\t1\t0.0\t4\t1"
## [182] "110\t2\t0.0\t4\t2"
## [183] "112\t2\t0.0\t4\t2"
## [184] "113\t2\t0.0\t4\t2"
## [185] "114\t2\t0.0\t4\t2"
## [186] "115\t1\t0.0\t4\t1"
## [187] "118\t1\t0.0\t4\t1"
## [188] "121\t1\t0.0\t4\t1"
## [189] "126\t1\t0.0\t4\t0 0 0 0 1"
## [190] "127\t2\t0.0\t4\t1 0 0 1"
## [191] "131\t1\t0.0\t4\t1"
## [192] "134\t1\t0.0\t4\t0 0 0 1"
## [193] "135\t1\t0.0\t4\t1"
## [194] "138\t2\t0.0\t4\t2"
## [195] "139\t2\t0.0\t4\t2"
## [196] "140\t3\t0.0\t4\t3"
## [197] "141\t2\t0.0\t4\t2"
## [198] "143\t1\t0.0\t4\t1"
## [199] "146\t2\t0.0\t4\t2"
## [200] "147\t1\t0.0\t4\t1"
## [201] "148\t1\t0.0\t4\t0 1"
## [202] "151\t1\t0.0\t4\t0 0 0 1"
## [203] "152\t1\t0.0\t4\t1"
## [204] "161\t1\t0.0\t4\t1"
## [205] "173\t1\t0.0\t4\t1"
## [206] "190\t1\t0.0\t4\t0 1"
##
## [[31]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1883_S31_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1883_S31_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1883_S31_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1883_S31_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.28 s (131 us/read; 0.46 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 9,767"
## [9] " Read 1 with adapter: 81 (0.8%)"
## [10] " Read 2 with adapter: 327 (3.3%)"
## [11] "Pairs written (passing filters): 9,767 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 4,102,140 bp"
## [14] " Read 1: 1,914,332 bp"
## [15] " Read 2: 2,187,808 bp"
## [16] "Total written (filtered): 4,079,675 bp (99.5%)"
## [17] " Read 1: 1,912,267 bp"
## [18] " Read 2: 2,167,408 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 75 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "6\t1\t2.4\t0\t1"
## [30] "12\t1\t0.0\t1\t1"
## [31] "15\t1\t0.0\t1\t1"
## [32] "16\t7\t0.0\t1\t4 3"
## [33] "17\t35\t0.0\t1\t31 4"
## [34] "26\t1\t0.0\t2\t1"
## [35] "27\t1\t0.0\t2\t1"
## [36] "28\t1\t0.0\t2\t1"
## [37] "29\t1\t0.0\t2\t1"
## [38] "30\t2\t0.0\t3\t0 2"
## [39] "31\t19\t0.0\t3\t13 6"
## [40] "48\t3\t0.0\t4\t0 0 2 1"
## [41] "61\t1\t0.0\t4\t0 1"
## [42] "62\t1\t0.0\t4\t0 1"
## [43] ""
## [44] ""
## [45] "=== First read: Adapter 2 ==="
## [46] ""
## [47] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 6 times"
## [48] ""
## [49] "No. of allowed errors:"
## [50] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [51] ""
## [52] "Bases preceding removed adapters:"
## [53] " A: 16.7%"
## [54] " C: 0.0%"
## [55] " G: 83.3%"
## [56] " T: 0.0%"
## [57] " none/other: 0.0%"
## [58] ""
## [59] "Overview of removed sequences"
## [60] "length\tcount\texpect\tmax.err\terror counts"
## [61] "17\t1\t0.0\t1\t1"
## [62] "33\t1\t0.0\t2\t1"
## [63] "34\t1\t0.0\t2\t1"
## [64] "38\t1\t0.0\t2\t1"
## [65] "82\t1\t0.0\t2\t1"
## [66] "95\t1\t0.0\t2\t1"
## [67] ""
## [68] ""
## [69] "=== Second read: Adapter 3 ==="
## [70] ""
## [71] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 4 times"
## [72] ""
## [73] "No. of allowed errors:"
## [74] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [75] ""
## [76] "Overview of removed sequences"
## [77] "length\tcount\texpect\tmax.err\terror counts"
## [78] "17\t1\t0.0\t1\t1"
## [79] "20\t1\t0.0\t2\t1"
## [80] "29\t1\t0.0\t2\t1"
## [81] "73\t1\t0.0\t2\t1"
## [82] ""
## [83] ""
## [84] "=== Second read: Adapter 4 ==="
## [85] ""
## [86] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 323 times"
## [87] ""
## [88] "No. of allowed errors:"
## [89] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [90] ""
## [91] "Bases preceding removed adapters:"
## [92] " A: 61.6%"
## [93] " C: 27.6%"
## [94] " G: 5.9%"
## [95] " T: 5.0%"
## [96] " none/other: 0.0%"
## [97] ""
## [98] "Overview of removed sequences"
## [99] "length\tcount\texpect\tmax.err\terror counts"
## [100] "5\t10\t9.5\t0\t10"
## [101] "7\t2\t0.6\t0\t2"
## [102] "8\t10\t0.1\t0\t10"
## [103] "9\t3\t0.0\t0\t3"
## [104] "10\t2\t0.0\t1\t2"
## [105] "11\t3\t0.0\t1\t3"
## [106] "12\t1\t0.0\t1\t0 1"
## [107] "13\t5\t0.0\t1\t4 1"
## [108] "14\t5\t0.0\t1\t5"
## [109] "15\t1\t0.0\t1\t1"
## [110] "16\t4\t0.0\t1\t3 1"
## [111] "17\t3\t0.0\t1\t3"
## [112] "18\t1\t0.0\t1\t1"
## [113] "19\t6\t0.0\t1\t6"
## [114] "20\t5\t0.0\t2\t5"
## [115] "21\t11\t0.0\t2\t6 3 2"
## [116] "22\t1\t0.0\t2\t1"
## [117] "23\t4\t0.0\t2\t2 2"
## [118] "24\t2\t0.0\t2\t2"
## [119] "25\t1\t0.0\t2\t1"
## [120] "26\t1\t0.0\t2\t1"
## [121] "27\t1\t0.0\t2\t0 1"
## [122] "30\t3\t0.0\t3\t3"
## [123] "31\t3\t0.0\t3\t2 0 1"
## [124] "32\t3\t0.0\t3\t2 0 0 1"
## [125] "33\t4\t0.0\t3\t3 1"
## [126] "34\t3\t0.0\t3\t2 1"
## [127] "35\t4\t0.0\t3\t2 2"
## [128] "37\t2\t0.0\t3\t1 1"
## [129] "38\t1\t0.0\t3\t0 1"
## [130] "39\t1\t0.0\t3\t1"
## [131] "41\t1\t0.0\t4\t0 0 1"
## [132] "42\t5\t0.0\t4\t3 1 0 0 1"
## [133] "43\t5\t0.0\t4\t4 1"
## [134] "45\t5\t0.0\t4\t5"
## [135] "46\t1\t0.0\t4\t1"
## [136] "47\t6\t0.0\t4\t6"
## [137] "48\t5\t0.0\t4\t4 0 0 0 1"
## [138] "49\t2\t0.0\t4\t2"
## [139] "50\t4\t0.0\t4\t3 1"
## [140] "51\t6\t0.0\t4\t4 1 0 1"
## [141] "52\t6\t0.0\t4\t4 1 1"
## [142] "54\t5\t0.0\t4\t4 0 0 1"
## [143] "55\t3\t0.0\t4\t1 2"
## [144] "57\t2\t0.0\t4\t1 0 0 1"
## [145] "58\t2\t0.0\t4\t2"
## [146] "60\t6\t0.0\t4\t2 1 0 3"
## [147] "61\t1\t0.0\t4\t1"
## [148] "62\t1\t0.0\t4\t1"
## [149] "63\t5\t0.0\t4\t5"
## [150] "64\t4\t0.0\t4\t4"
## [151] "65\t4\t0.0\t4\t1 1 0 1 1"
## [152] "66\t5\t0.0\t4\t5"
## [153] "67\t3\t0.0\t4\t2 0 1"
## [154] "69\t1\t0.0\t4\t1"
## [155] "71\t2\t0.0\t4\t1 1"
## [156] "72\t2\t0.0\t4\t2"
## [157] "73\t1\t0.0\t4\t1"
## [158] "74\t4\t0.0\t4\t3 0 0 0 1"
## [159] "75\t2\t0.0\t4\t0 1 1"
## [160] "76\t2\t0.0\t4\t1 0 0 0 1"
## [161] "77\t4\t0.0\t4\t3 1"
## [162] "79\t2\t0.0\t4\t2"
## [163] "80\t3\t0.0\t4\t2 1"
## [164] "81\t1\t0.0\t4\t0 1"
## [165] "82\t1\t0.0\t4\t1"
## [166] "84\t3\t0.0\t4\t3"
## [167] "85\t5\t0.0\t4\t4 0 1"
## [168] "86\t3\t0.0\t4\t2 1"
## [169] "87\t2\t0.0\t4\t2"
## [170] "88\t7\t0.0\t4\t5 0 0 2"
## [171] "89\t1\t0.0\t4\t1"
## [172] "92\t1\t0.0\t4\t1"
## [173] "93\t2\t0.0\t4\t2"
## [174] "94\t6\t0.0\t4\t6"
## [175] "95\t3\t0.0\t4\t2 1"
## [176] "96\t2\t0.0\t4\t2"
## [177] "97\t2\t0.0\t4\t2"
## [178] "98\t2\t0.0\t4\t2"
## [179] "99\t2\t0.0\t4\t2"
## [180] "101\t2\t0.0\t4\t2"
## [181] "102\t2\t0.0\t4\t1 0 0 1"
## [182] "103\t4\t0.0\t4\t1 2 1"
## [183] "104\t3\t0.0\t4\t3"
## [184] "105\t4\t0.0\t4\t4"
## [185] "107\t2\t0.0\t4\t2"
## [186] "108\t1\t0.0\t4\t0 0 0 1"
## [187] "109\t1\t0.0\t4\t0 0 0 1"
## [188] "110\t2\t0.0\t4\t2"
## [189] "111\t2\t0.0\t4\t2"
## [190] "112\t2\t0.0\t4\t2"
## [191] "113\t2\t0.0\t4\t1 1"
## [192] "114\t1\t0.0\t4\t0 1"
## [193] "115\t1\t0.0\t4\t1"
## [194] "116\t1\t0.0\t4\t1"
## [195] "117\t2\t0.0\t4\t0 1 0 0 1"
## [196] "118\t1\t0.0\t4\t1"
## [197] "120\t1\t0.0\t4\t1"
## [198] "121\t3\t0.0\t4\t2 0 0 1"
## [199] "125\t2\t0.0\t4\t2"
## [200] "126\t1\t0.0\t4\t0 0 0 1"
## [201] "127\t1\t0.0\t4\t1"
## [202] "129\t1\t0.0\t4\t0 1"
## [203] "134\t2\t0.0\t4\t1 1"
## [204] "136\t1\t0.0\t4\t1"
## [205] "139\t1\t0.0\t4\t1"
## [206] "140\t2\t0.0\t4\t2"
## [207] "141\t2\t0.0\t4\t1 0 0 0 1"
## [208] "144\t1\t0.0\t4\t1"
## [209] "146\t1\t0.0\t4\t0 1"
## [210] "147\t1\t0.0\t4\t1"
## [211] "148\t3\t0.0\t4\t3"
## [212] "150\t1\t0.0\t4\t1"
## [213] "152\t2\t0.0\t4\t1 1"
## [214] "154\t1\t0.0\t4\t1"
## [215] "161\t1\t0.0\t4\t0 0 0 0 1"
## [216] "167\t1\t0.0\t4\t1"
## [217] "171\t1\t0.0\t4\t1"
## [218] "174\t1\t0.0\t4\t1"
##
## [[32]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1884_S32_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1884_S32_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1884_S32_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1884_S32_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 2.10 s (120 us/read; 0.50 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 17,599"
## [9] " Read 1 with adapter: 23 (0.1%)"
## [10] " Read 2 with adapter: 147 (0.8%)"
## [11] "Pairs written (passing filters): 17,599 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 7,391,580 bp"
## [14] " Read 1: 3,449,404 bp"
## [15] " Read 2: 3,942,176 bp"
## [16] "Total written (filtered): 7,382,734 bp (99.9%)"
## [17] " Read 1: 3,448,755 bp"
## [18] " Read 2: 3,933,979 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 22 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "8\t1\t0.3\t0\t1"
## [30] "17\t10\t0.0\t1\t10"
## [31] "21\t1\t0.0\t2\t1"
## [32] "30\t4\t0.0\t3\t3 1"
## [33] "31\t5\t0.0\t3\t4 1"
## [34] "93\t1\t0.0\t4\t0 0 0 1"
## [35] ""
## [36] ""
## [37] "=== First read: Adapter 2 ==="
## [38] ""
## [39] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 1 times"
## [40] ""
## [41] "No. of allowed errors:"
## [42] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [43] ""
## [44] "Bases preceding removed adapters:"
## [45] " A: 0.0%"
## [46] " C: 100.0%"
## [47] " G: 0.0%"
## [48] " T: 0.0%"
## [49] " none/other: 0.0%"
## [50] ""
## [51] "Overview of removed sequences"
## [52] "length\tcount\texpect\tmax.err\terror counts"
## [53] "82\t1\t0.0\t2\t1"
## [54] ""
## [55] ""
## [56] "=== Second read: Adapter 3 ==="
## [57] ""
## [58] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [59] ""
## [60] "No. of allowed errors:"
## [61] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [62] ""
## [63] "Overview of removed sequences"
## [64] "length\tcount\texpect\tmax.err\terror counts"
## [65] "6\t1\t4.3\t0\t1"
## [66] ""
## [67] ""
## [68] "=== Second read: Adapter 4 ==="
## [69] ""
## [70] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 147 times"
## [71] ""
## [72] "No. of allowed errors:"
## [73] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [74] ""
## [75] "Bases preceding removed adapters:"
## [76] " A: 61.2%"
## [77] " C: 24.5%"
## [78] " G: 5.4%"
## [79] " T: 8.8%"
## [80] " none/other: 0.0%"
## [81] ""
## [82] "Overview of removed sequences"
## [83] "length\tcount\texpect\tmax.err\terror counts"
## [84] "5\t12\t17.2\t0\t12"
## [85] "6\t2\t4.3\t0\t2"
## [86] "7\t1\t1.1\t0\t1"
## [87] "8\t5\t0.3\t0\t5"
## [88] "9\t3\t0.1\t0\t3"
## [89] "11\t1\t0.0\t1\t0 1"
## [90] "13\t1\t0.0\t1\t1"
## [91] "14\t2\t0.0\t1\t1 1"
## [92] "15\t1\t0.0\t1\t1"
## [93] "16\t2\t0.0\t1\t2"
## [94] "18\t1\t0.0\t1\t1"
## [95] "19\t1\t0.0\t1\t1"
## [96] "20\t1\t0.0\t2\t1"
## [97] "21\t7\t0.0\t2\t4 2 1"
## [98] "22\t1\t0.0\t2\t1"
## [99] "23\t1\t0.0\t2\t1"
## [100] "26\t2\t0.0\t2\t1 1"
## [101] "28\t1\t0.0\t2\t1"
## [102] "29\t3\t0.0\t2\t3"
## [103] "31\t1\t0.0\t3\t0 1"
## [104] "33\t2\t0.0\t3\t1 0 1"
## [105] "34\t3\t0.0\t3\t2 1"
## [106] "35\t2\t0.0\t3\t1 1"
## [107] "37\t1\t0.0\t3\t0 0 0 1"
## [108] "38\t1\t0.0\t3\t1"
## [109] "39\t2\t0.0\t3\t1 1"
## [110] "42\t1\t0.0\t4\t1"
## [111] "44\t2\t0.0\t4\t2"
## [112] "48\t2\t0.0\t4\t2"
## [113] "51\t3\t0.0\t4\t2 1"
## [114] "52\t1\t0.0\t4\t1"
## [115] "53\t2\t0.0\t4\t1 1"
## [116] "55\t3\t0.0\t4\t3"
## [117] "58\t1\t0.0\t4\t0 1"
## [118] "59\t2\t0.0\t4\t2"
## [119] "60\t3\t0.0\t4\t3"
## [120] "61\t1\t0.0\t4\t0 1"
## [121] "62\t1\t0.0\t4\t1"
## [122] "63\t2\t0.0\t4\t2"
## [123] "64\t7\t0.0\t4\t5 2"
## [124] "65\t1\t0.0\t4\t1"
## [125] "66\t1\t0.0\t4\t1"
## [126] "67\t1\t0.0\t4\t1"
## [127] "69\t1\t0.0\t4\t1"
## [128] "72\t2\t0.0\t4\t1 0 0 1"
## [129] "77\t2\t0.0\t4\t2"
## [130] "78\t2\t0.0\t4\t1 1"
## [131] "82\t1\t0.0\t4\t1"
## [132] "83\t2\t0.0\t4\t1 1"
## [133] "84\t4\t0.0\t4\t4"
## [134] "86\t3\t0.0\t4\t3"
## [135] "88\t2\t0.0\t4\t1 0 0 1"
## [136] "89\t1\t0.0\t4\t1"
## [137] "90\t1\t0.0\t4\t1"
## [138] "91\t1\t0.0\t4\t1"
## [139] "92\t1\t0.0\t4\t1"
## [140] "94\t1\t0.0\t4\t1"
## [141] "96\t1\t0.0\t4\t1"
## [142] "97\t2\t0.0\t4\t2"
## [143] "98\t2\t0.0\t4\t2"
## [144] "99\t1\t0.0\t4\t1"
## [145] "100\t1\t0.0\t4\t1"
## [146] "102\t1\t0.0\t4\t1"
## [147] "104\t3\t0.0\t4\t1 0 0 2"
## [148] "105\t4\t0.0\t4\t4"
## [149] "106\t1\t0.0\t4\t1"
## [150] "107\t1\t0.0\t4\t1"
## [151] "108\t1\t0.0\t4\t0 0 1"
## [152] "110\t1\t0.0\t4\t1"
## [153] "112\t1\t0.0\t4\t1"
## [154] "113\t1\t0.0\t4\t1"
## [155] "115\t2\t0.0\t4\t2"
## [156] "119\t2\t0.0\t4\t1 0 1"
## [157] "121\t1\t0.0\t4\t1"
## [158] "127\t1\t0.0\t4\t1"
## [159] "129\t1\t0.0\t4\t1"
## [160] "138\t1\t0.0\t4\t1"
##
## [[33]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1885_S33_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1885_S33_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1885_S33_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1885_S33_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.73 s (120 us/read; 0.50 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 14,416"
## [9] " Read 1 with adapter: 9 (0.1%)"
## [10] " Read 2 with adapter: 111 (0.8%)"
## [11] "Pairs written (passing filters): 14,416 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 6,054,720 bp"
## [14] " Read 1: 2,825,536 bp"
## [15] " Read 2: 3,229,184 bp"
## [16] "Total written (filtered): 6,049,090 bp (99.9%)"
## [17] " Read 1: 2,825,183 bp"
## [18] " Read 2: 3,223,907 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "17\t1\t0.0\t1\t1"
## [30] "31\t1\t0.0\t3\t1"
## [31] "79\t1\t0.0\t4\t0 0 1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 6 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 16.7%"
## [43] " C: 0.0%"
## [44] " G: 83.3%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "8\t1\t0.2\t0\t1"
## [51] "18\t1\t0.0\t1\t1"
## [52] "32\t1\t0.0\t2\t1"
## [53] "38\t2\t0.0\t2\t2"
## [54] "92\t1\t0.0\t2\t1"
## [55] ""
## [56] ""
## [57] "=== Second read: Adapter 3 ==="
## [58] ""
## [59] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 2 times"
## [60] ""
## [61] "No. of allowed errors:"
## [62] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [63] ""
## [64] "Overview of removed sequences"
## [65] "length\tcount\texpect\tmax.err\terror counts"
## [66] "6\t1\t3.5\t0\t1"
## [67] "26\t1\t0.0\t2\t1"
## [68] ""
## [69] ""
## [70] "=== Second read: Adapter 4 ==="
## [71] ""
## [72] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 111 times"
## [73] ""
## [74] "No. of allowed errors:"
## [75] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [76] ""
## [77] "Bases preceding removed adapters:"
## [78] " A: 59.5%"
## [79] " C: 31.5%"
## [80] " G: 5.4%"
## [81] " T: 3.6%"
## [82] " none/other: 0.0%"
## [83] ""
## [84] "Overview of removed sequences"
## [85] "length\tcount\texpect\tmax.err\terror counts"
## [86] "5\t13\t14.1\t0\t13"
## [87] "6\t2\t3.5\t0\t2"
## [88] "8\t7\t0.2\t0\t7"
## [89] "9\t2\t0.1\t0\t2"
## [90] "10\t2\t0.0\t1\t2"
## [91] "11\t2\t0.0\t1\t2"
## [92] "14\t2\t0.0\t1\t1 1"
## [93] "15\t1\t0.0\t1\t1"
## [94] "16\t2\t0.0\t1\t1 1"
## [95] "17\t1\t0.0\t1\t1"
## [96] "20\t3\t0.0\t2\t3"
## [97] "23\t2\t0.0\t2\t1 1"
## [98] "24\t1\t0.0\t2\t1"
## [99] "25\t1\t0.0\t2\t0 0 1"
## [100] "26\t1\t0.0\t2\t1"
## [101] "27\t1\t0.0\t2\t1"
## [102] "28\t2\t0.0\t2\t2"
## [103] "29\t1\t0.0\t2\t0 0 1"
## [104] "31\t1\t0.0\t3\t1"
## [105] "33\t1\t0.0\t3\t1"
## [106] "34\t3\t0.0\t3\t2 0 1"
## [107] "35\t1\t0.0\t3\t1"
## [108] "41\t1\t0.0\t4\t0 1"
## [109] "42\t3\t0.0\t4\t2 1"
## [110] "43\t2\t0.0\t4\t2"
## [111] "44\t1\t0.0\t4\t1"
## [112] "45\t1\t0.0\t4\t0 1"
## [113] "48\t1\t0.0\t4\t1"
## [114] "50\t3\t0.0\t4\t2 1"
## [115] "51\t1\t0.0\t4\t1"
## [116] "52\t2\t0.0\t4\t1 1"
## [117] "54\t1\t0.0\t4\t1"
## [118] "55\t2\t0.0\t4\t1 0 1"
## [119] "56\t1\t0.0\t4\t1"
## [120] "57\t1\t0.0\t4\t1"
## [121] "60\t1\t0.0\t4\t1"
## [122] "63\t2\t0.0\t4\t2"
## [123] "64\t1\t0.0\t4\t0 1"
## [124] "66\t3\t0.0\t4\t3"
## [125] "67\t1\t0.0\t4\t1"
## [126] "71\t1\t0.0\t4\t1"
## [127] "72\t2\t0.0\t4\t2"
## [128] "74\t1\t0.0\t4\t1"
## [129] "76\t2\t0.0\t4\t1 0 0 1"
## [130] "77\t1\t0.0\t4\t1"
## [131] "78\t2\t0.0\t4\t1 0 1"
## [132] "79\t1\t0.0\t4\t0 1"
## [133] "81\t1\t0.0\t4\t1"
## [134] "84\t1\t0.0\t4\t1"
## [135] "85\t1\t0.0\t4\t1"
## [136] "86\t1\t0.0\t4\t1"
## [137] "88\t1\t0.0\t4\t1"
## [138] "91\t1\t0.0\t4\t1"
## [139] "92\t1\t0.0\t4\t1"
## [140] "98\t1\t0.0\t4\t1"
## [141] "104\t1\t0.0\t4\t1"
## [142] "105\t2\t0.0\t4\t2"
## [143] "107\t1\t0.0\t4\t0 0 0 1"
## [144] "108\t1\t0.0\t4\t1"
## [145] "116\t1\t0.0\t4\t1"
## [146] "119\t1\t0.0\t4\t1"
## [147] "120\t1\t0.0\t4\t1"
## [148] "121\t1\t0.0\t4\t1"
## [149] "123\t2\t0.0\t4\t2"
## [150] "126\t1\t0.0\t4\t1"
## [151] "144\t1\t0.0\t4\t1"
##
## [[34]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1886_S34_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1886_S34_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1886_S34_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1886_S34_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 2.32 s (121 us/read; 0.49 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 19,137"
## [9] " Read 1 with adapter: 3 (0.0%)"
## [10] " Read 2 with adapter: 117 (0.6%)"
## [11] "Pairs written (passing filters): 19,137 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 8,037,540 bp"
## [14] " Read 1: 3,750,852 bp"
## [15] " Read 2: 4,286,688 bp"
## [16] "Total written (filtered): 8,031,739 bp (99.9%)"
## [17] " Read 1: 3,750,799 bp"
## [18] " Read 2: 4,280,940 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t18.7\t0\t1"
## [30] "14\t1\t0.0\t1\t1"
## [31] "34\t1\t0.0\t3\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 0 times"
## [37] ""
## [38] "=== Second read: Adapter 3 ==="
## [39] ""
## [40] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 3 times"
## [41] ""
## [42] "No. of allowed errors:"
## [43] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [44] ""
## [45] "Overview of removed sequences"
## [46] "length\tcount\texpect\tmax.err\terror counts"
## [47] "5\t1\t18.7\t0\t1"
## [48] "12\t1\t0.0\t1\t1"
## [49] "21\t1\t0.0\t2\t1"
## [50] ""
## [51] ""
## [52] "=== Second read: Adapter 4 ==="
## [53] ""
## [54] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 115 times"
## [55] ""
## [56] "No. of allowed errors:"
## [57] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [58] ""
## [59] "Bases preceding removed adapters:"
## [60] " A: 59.1%"
## [61] " C: 29.6%"
## [62] " G: 8.7%"
## [63] " T: 2.6%"
## [64] " none/other: 0.0%"
## [65] ""
## [66] "Overview of removed sequences"
## [67] "length\tcount\texpect\tmax.err\terror counts"
## [68] "5\t14\t18.7\t0\t14"
## [69] "6\t2\t4.7\t0\t2"
## [70] "8\t4\t0.3\t0\t4"
## [71] "9\t2\t0.1\t0\t2"
## [72] "11\t1\t0.0\t1\t1"
## [73] "14\t1\t0.0\t1\t1"
## [74] "15\t2\t0.0\t1\t2"
## [75] "16\t3\t0.0\t1\t2 1"
## [76] "17\t6\t0.0\t1\t6"
## [77] "19\t1\t0.0\t1\t0 1"
## [78] "20\t1\t0.0\t2\t1"
## [79] "21\t1\t0.0\t2\t1"
## [80] "22\t3\t0.0\t2\t2 0 1"
## [81] "23\t1\t0.0\t2\t0 1"
## [82] "24\t1\t0.0\t2\t1"
## [83] "26\t1\t0.0\t2\t1"
## [84] "27\t1\t0.0\t2\t1"
## [85] "28\t2\t0.0\t2\t1 0 1"
## [86] "29\t1\t0.0\t2\t1"
## [87] "31\t1\t0.0\t3\t1"
## [88] "32\t2\t0.0\t3\t2"
## [89] "35\t4\t0.0\t3\t4"
## [90] "37\t1\t0.0\t3\t1"
## [91] "40\t1\t0.0\t4\t1"
## [92] "41\t2\t0.0\t4\t2"
## [93] "42\t2\t0.0\t4\t1 1"
## [94] "43\t1\t0.0\t4\t1"
## [95] "45\t1\t0.0\t4\t0 1"
## [96] "51\t1\t0.0\t4\t1"
## [97] "52\t2\t0.0\t4\t2"
## [98] "53\t2\t0.0\t4\t2"
## [99] "54\t4\t0.0\t4\t3 1"
## [100] "56\t1\t0.0\t4\t0 1"
## [101] "57\t1\t0.0\t4\t1"
## [102] "58\t2\t0.0\t4\t2"
## [103] "61\t1\t0.0\t4\t1"
## [104] "62\t1\t0.0\t4\t1"
## [105] "63\t2\t0.0\t4\t2"
## [106] "66\t1\t0.0\t4\t1"
## [107] "73\t2\t0.0\t4\t2"
## [108] "74\t4\t0.0\t4\t4"
## [109] "75\t1\t0.0\t4\t1"
## [110] "79\t2\t0.0\t4\t2"
## [111] "82\t1\t0.0\t4\t1"
## [112] "84\t1\t0.0\t4\t1"
## [113] "85\t1\t0.0\t4\t1"
## [114] "90\t1\t0.0\t4\t1"
## [115] "93\t1\t0.0\t4\t1"
## [116] "94\t1\t0.0\t4\t1"
## [117] "97\t1\t0.0\t4\t1"
## [118] "100\t1\t0.0\t4\t1"
## [119] "101\t1\t0.0\t4\t1"
## [120] "103\t1\t0.0\t4\t1"
## [121] "104\t2\t0.0\t4\t2"
## [122] "105\t1\t0.0\t4\t0 1"
## [123] "107\t1\t0.0\t4\t0 1"
## [124] "108\t1\t0.0\t4\t1"
## [125] "109\t1\t0.0\t4\t1"
## [126] "113\t2\t0.0\t4\t2"
## [127] "120\t1\t0.0\t4\t1"
## [128] "125\t1\t0.0\t4\t1"
## [129] "139\t1\t0.0\t4\t1"
## [130] "149\t1\t0.0\t4\t1"
## [131] "154\t1\t0.0\t4\t1"
## [132] "156\t1\t0.0\t4\t1"
## [133] "165\t1\t0.0\t4\t1"
##
## [[35]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/1887_S35_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/1887_S35_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/1887_S35_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/1887_S35_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 2.08 s (121 us/read; 0.50 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 17,213"
## [9] " Read 1 with adapter: 10 (0.1%)"
## [10] " Read 2 with adapter: 147 (0.9%)"
## [11] "Pairs written (passing filters): 17,213 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 7,229,460 bp"
## [14] " Read 1: 3,373,748 bp"
## [15] " Read 2: 3,855,712 bp"
## [16] "Total written (filtered): 7,219,994 bp (99.9%)"
## [17] " Read 1: 3,373,639 bp"
## [18] " Read 2: 3,846,355 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 4 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t2\t16.8\t0\t2"
## [30] "24\t1\t0.0\t2\t0 1"
## [31] "25\t1\t0.0\t2\t0 1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 6 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 100.0%"
## [43] " C: 0.0%"
## [44] " G: 0.0%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "6\t1\t4.2\t0\t1"
## [51] "7\t1\t1.1\t0\t1"
## [52] "9\t3\t0.1\t0\t1 2"
## [53] "10\t1\t0.0\t1\t0 1"
## [54] ""
## [55] ""
## [56] "=== Second read: Adapter 3 ==="
## [57] ""
## [58] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [59] ""
## [60] "No. of allowed errors:"
## [61] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [62] ""
## [63] "Overview of removed sequences"
## [64] "length\tcount\texpect\tmax.err\terror counts"
## [65] "6\t1\t4.2\t0\t1"
## [66] ""
## [67] ""
## [68] "=== Second read: Adapter 4 ==="
## [69] ""
## [70] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 146 times"
## [71] ""
## [72] "No. of allowed errors:"
## [73] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [74] ""
## [75] "Bases preceding removed adapters:"
## [76] " A: 67.1%"
## [77] " C: 24.0%"
## [78] " G: 4.1%"
## [79] " T: 4.8%"
## [80] " none/other: 0.0%"
## [81] ""
## [82] "Overview of removed sequences"
## [83] "length\tcount\texpect\tmax.err\terror counts"
## [84] "5\t8\t16.8\t0\t8"
## [85] "6\t1\t4.2\t0\t1"
## [86] "7\t1\t1.1\t0\t1"
## [87] "9\t2\t0.1\t0\t2"
## [88] "10\t1\t0.0\t1\t1"
## [89] "14\t3\t0.0\t1\t3"
## [90] "16\t1\t0.0\t1\t1"
## [91] "17\t2\t0.0\t1\t2"
## [92] "19\t1\t0.0\t1\t1"
## [93] "20\t2\t0.0\t2\t2"
## [94] "21\t4\t0.0\t2\t0 3 1"
## [95] "22\t1\t0.0\t2\t1"
## [96] "23\t2\t0.0\t2\t2"
## [97] "25\t3\t0.0\t2\t2 0 1"
## [98] "26\t3\t0.0\t2\t3"
## [99] "29\t1\t0.0\t2\t1"
## [100] "30\t1\t0.0\t3\t1"
## [101] "33\t2\t0.0\t3\t2"
## [102] "34\t2\t0.0\t3\t1 1"
## [103] "35\t3\t0.0\t3\t1 1 0 1"
## [104] "36\t2\t0.0\t3\t1 0 1"
## [105] "41\t2\t0.0\t4\t2"
## [106] "42\t1\t0.0\t4\t1"
## [107] "43\t2\t0.0\t4\t2"
## [108] "44\t1\t0.0\t4\t0 0 1"
## [109] "45\t2\t0.0\t4\t1 1"
## [110] "46\t4\t0.0\t4\t4"
## [111] "48\t1\t0.0\t4\t1"
## [112] "50\t1\t0.0\t4\t1"
## [113] "51\t1\t0.0\t4\t0 1"
## [114] "54\t1\t0.0\t4\t1"
## [115] "55\t2\t0.0\t4\t2"
## [116] "57\t4\t0.0\t4\t4"
## [117] "58\t4\t0.0\t4\t4"
## [118] "62\t1\t0.0\t4\t1"
## [119] "65\t3\t0.0\t4\t3"
## [120] "66\t1\t0.0\t4\t0 1"
## [121] "69\t1\t0.0\t4\t1"
## [122] "70\t3\t0.0\t4\t3"
## [123] "71\t1\t0.0\t4\t0 1"
## [124] "72\t2\t0.0\t4\t2"
## [125] "75\t1\t0.0\t4\t1"
## [126] "76\t2\t0.0\t4\t2"
## [127] "77\t1\t0.0\t4\t1"
## [128] "79\t5\t0.0\t4\t3 2"
## [129] "80\t2\t0.0\t4\t2"
## [130] "81\t1\t0.0\t4\t1"
## [131] "82\t3\t0.0\t4\t2 1"
## [132] "83\t1\t0.0\t4\t1"
## [133] "84\t2\t0.0\t4\t2"
## [134] "85\t3\t0.0\t4\t3"
## [135] "86\t1\t0.0\t4\t1"
## [136] "89\t1\t0.0\t4\t1"
## [137] "91\t1\t0.0\t4\t1"
## [138] "92\t3\t0.0\t4\t3"
## [139] "94\t1\t0.0\t4\t0 1"
## [140] "96\t2\t0.0\t4\t2"
## [141] "98\t2\t0.0\t4\t1 1"
## [142] "99\t1\t0.0\t4\t1"
## [143] "101\t2\t0.0\t4\t1 1"
## [144] "102\t1\t0.0\t4\t1"
## [145] "103\t1\t0.0\t4\t1"
## [146] "104\t1\t0.0\t4\t1"
## [147] "105\t3\t0.0\t4\t3"
## [148] "108\t1\t0.0\t4\t1"
## [149] "110\t1\t0.0\t4\t1"
## [150] "111\t1\t0.0\t4\t0 1"
## [151] "112\t1\t0.0\t4\t1"
## [152] "113\t1\t0.0\t4\t1"
## [153] "116\t2\t0.0\t4\t2"
## [154] "119\t2\t0.0\t4\t1 1"
## [155] "122\t1\t0.0\t4\t1"
## [156] "127\t1\t0.0\t4\t1"
## [157] "128\t1\t0.0\t4\t1"
## [158] "131\t1\t0.0\t4\t1"
## [159] "134\t1\t0.0\t4\t1"
## [160] "137\t1\t0.0\t4\t1"
## [161] "141\t1\t0.0\t4\t1"
## [162] "142\t1\t0.0\t4\t1"
## [163] "146\t2\t0.0\t4\t2"
## [164] "148\t1\t0.0\t4\t1"
## [165] "159\t1\t0.0\t4\t1"
##
## [[36]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/188RNA1_S36_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/188RNA1_S36_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/188RNA1_S36_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/188RNA1_S36_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.34 s (124 us/read; 0.48 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 2,776"
## [9] " Read 1 with adapter: 12 (0.4%)"
## [10] " Read 2 with adapter: 210 (7.6%)"
## [11] "Pairs written (passing filters): 2,776 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 1,165,920 bp"
## [14] " Read 1: 544,096 bp"
## [15] " Read 2: 621,824 bp"
## [16] "Total written (filtered): 1,149,566 bp (98.6%)"
## [17] " Read 1: 543,704 bp"
## [18] " Read 2: 605,862 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 6 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "16\t1\t0.0\t1\t1"
## [30] "17\t2\t0.0\t1\t2"
## [31] "30\t1\t0.0\t3\t1"
## [32] "31\t1\t0.0\t3\t1"
## [33] "49\t1\t0.0\t4\t0 0 1"
## [34] ""
## [35] ""
## [36] "=== First read: Adapter 2 ==="
## [37] ""
## [38] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 6 times"
## [39] ""
## [40] "No. of allowed errors:"
## [41] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [42] ""
## [43] "Bases preceding removed adapters:"
## [44] " A: 0.0%"
## [45] " C: 0.0%"
## [46] " G: 83.3%"
## [47] " T: 16.7%"
## [48] " none/other: 0.0%"
## [49] ""
## [50] "Overview of removed sequences"
## [51] "length\tcount\texpect\tmax.err\terror counts"
## [52] "6\t1\t0.7\t0\t1"
## [53] "28\t1\t0.0\t2\t1"
## [54] "36\t3\t0.0\t2\t3"
## [55] "90\t1\t0.0\t2\t1"
## [56] ""
## [57] ""
## [58] "=== Second read: Adapter 3 ==="
## [59] ""
## [60] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [61] ""
## [62] "=== Second read: Adapter 4 ==="
## [63] ""
## [64] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 210 times"
## [65] ""
## [66] "No. of allowed errors:"
## [67] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [68] ""
## [69] "Bases preceding removed adapters:"
## [70] " A: 55.2%"
## [71] " C: 35.2%"
## [72] " G: 6.7%"
## [73] " T: 2.9%"
## [74] " none/other: 0.0%"
## [75] ""
## [76] "Overview of removed sequences"
## [77] "length\tcount\texpect\tmax.err\terror counts"
## [78] "6\t1\t0.7\t0\t1"
## [79] "7\t2\t0.2\t0\t2"
## [80] "8\t4\t0.0\t0\t4"
## [81] "9\t2\t0.0\t0\t2"
## [82] "12\t1\t0.0\t1\t1"
## [83] "13\t1\t0.0\t1\t1"
## [84] "14\t2\t0.0\t1\t1 1"
## [85] "16\t2\t0.0\t1\t2"
## [86] "20\t2\t0.0\t2\t2"
## [87] "21\t1\t0.0\t2\t1"
## [88] "22\t1\t0.0\t2\t1"
## [89] "24\t1\t0.0\t2\t0 0 1"
## [90] "25\t4\t0.0\t2\t3 1"
## [91] "26\t1\t0.0\t2\t0 1"
## [92] "27\t2\t0.0\t2\t2"
## [93] "28\t4\t0.0\t2\t3 1"
## [94] "29\t1\t0.0\t2\t1"
## [95] "32\t1\t0.0\t3\t1"
## [96] "33\t1\t0.0\t3\t0 0 1"
## [97] "34\t1\t0.0\t3\t1"
## [98] "35\t1\t0.0\t3\t1"
## [99] "40\t2\t0.0\t4\t2"
## [100] "41\t2\t0.0\t4\t2"
## [101] "42\t3\t0.0\t4\t3"
## [102] "43\t1\t0.0\t4\t1"
## [103] "45\t2\t0.0\t4\t1 1"
## [104] "46\t4\t0.0\t4\t3 1"
## [105] "48\t1\t0.0\t4\t1"
## [106] "50\t1\t0.0\t4\t1"
## [107] "51\t2\t0.0\t4\t1 0 1"
## [108] "52\t4\t0.0\t4\t4"
## [109] "53\t3\t0.0\t4\t3"
## [110] "55\t2\t0.0\t4\t1 0 1"
## [111] "56\t5\t0.0\t4\t2 1 0 2"
## [112] "57\t1\t0.0\t4\t1"
## [113] "58\t3\t0.0\t4\t2 1"
## [114] "59\t3\t0.0\t4\t2 1"
## [115] "60\t2\t0.0\t4\t1 1"
## [116] "61\t3\t0.0\t4\t3"
## [117] "62\t1\t0.0\t4\t1"
## [118] "64\t3\t0.0\t4\t3"
## [119] "65\t4\t0.0\t4\t3 0 0 1"
## [120] "66\t1\t0.0\t4\t1"
## [121] "67\t1\t0.0\t4\t1"
## [122] "69\t2\t0.0\t4\t2"
## [123] "70\t2\t0.0\t4\t2"
## [124] "71\t2\t0.0\t4\t1 0 0 1"
## [125] "72\t1\t0.0\t4\t0 1"
## [126] "73\t1\t0.0\t4\t1"
## [127] "74\t4\t0.0\t4\t3 1"
## [128] "75\t4\t0.0\t4\t4"
## [129] "77\t1\t0.0\t4\t1"
## [130] "79\t2\t0.0\t4\t2"
## [131] "82\t1\t0.0\t4\t1"
## [132] "83\t1\t0.0\t4\t1"
## [133] "84\t3\t0.0\t4\t3"
## [134] "85\t3\t0.0\t4\t3"
## [135] "86\t8\t0.0\t4\t8"
## [136] "87\t2\t0.0\t4\t2"
## [137] "88\t4\t0.0\t4\t3 0 1"
## [138] "89\t3\t0.0\t4\t3"
## [139] "92\t3\t0.0\t4\t3"
## [140] "94\t9\t0.0\t4\t8 0 1"
## [141] "95\t3\t0.0\t4\t3"
## [142] "96\t1\t0.0\t4\t1"
## [143] "97\t1\t0.0\t4\t1"
## [144] "100\t3\t0.0\t4\t3"
## [145] "101\t1\t0.0\t4\t1"
## [146] "103\t1\t0.0\t4\t1"
## [147] "105\t3\t0.0\t4\t3"
## [148] "106\t2\t0.0\t4\t2"
## [149] "108\t1\t0.0\t4\t1"
## [150] "109\t1\t0.0\t4\t1"
## [151] "110\t2\t0.0\t4\t1 1"
## [152] "111\t3\t0.0\t4\t3"
## [153] "112\t3\t0.0\t4\t2 0 1"
## [154] "113\t2\t0.0\t4\t2"
## [155] "115\t3\t0.0\t4\t3"
## [156] "117\t4\t0.0\t4\t3 0 0 1"
## [157] "118\t2\t0.0\t4\t2"
## [158] "119\t1\t0.0\t4\t1"
## [159] "120\t4\t0.0\t4\t3 1"
## [160] "121\t1\t0.0\t4\t1"
## [161] "122\t1\t0.0\t4\t1"
## [162] "125\t2\t0.0\t4\t2"
## [163] "127\t3\t0.0\t4\t3"
## [164] "129\t1\t0.0\t4\t1"
## [165] "130\t1\t0.0\t4\t1"
## [166] "132\t1\t0.0\t4\t1"
## [167] "133\t1\t0.0\t4\t1"
## [168] "138\t2\t0.0\t4\t2"
## [169] "140\t1\t0.0\t4\t1"
## [170] "144\t1\t0.0\t4\t1"
## [171] "145\t2\t0.0\t4\t2"
## [172] "146\t1\t0.0\t4\t1"
## [173] "148\t1\t0.0\t4\t1"
## [174] "150\t1\t0.0\t4\t1"
## [175] "151\t1\t0.0\t4\t1"
## [176] "160\t1\t0.0\t4\t1"
## [177] "162\t1\t0.0\t4\t1"
##
## [[37]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/188RNA2_S37_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/188RNA2_S37_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/188RNA2_S37_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/188RNA2_S37_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.38 s (120 us/read; 0.50 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 3,178"
## [9] " Read 1 with adapter: 12 (0.4%)"
## [10] " Read 2 with adapter: 146 (4.6%)"
## [11] "Pairs written (passing filters): 3,176 (99.9%)"
## [12] ""
## [13] "Total basepairs processed: 1,334,760 bp"
## [14] " Read 1: 622,888 bp"
## [15] " Read 2: 711,872 bp"
## [16] "Total written (filtered): 1,323,707 bp (99.2%)"
## [17] " Read 1: 622,114 bp"
## [18] " Read 2: 701,593 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 2 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "11\t1\t0.0\t1\t1"
## [30] "15\t1\t0.0\t1\t1"
## [31] ""
## [32] ""
## [33] "=== First read: Adapter 2 ==="
## [34] ""
## [35] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 10 times"
## [36] ""
## [37] "No. of allowed errors:"
## [38] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [39] ""
## [40] "Bases preceding removed adapters:"
## [41] " A: 60.0%"
## [42] " C: 0.0%"
## [43] " G: 40.0%"
## [44] " T: 0.0%"
## [45] " none/other: 0.0%"
## [46] ""
## [47] "Overview of removed sequences"
## [48] "length\tcount\texpect\tmax.err\terror counts"
## [49] "5\t1\t3.1\t0\t1"
## [50] "15\t1\t0.0\t1\t1"
## [51] "20\t1\t0.0\t2\t1"
## [52] "36\t3\t0.0\t2\t3"
## [53] "37\t1\t0.0\t2\t0 1"
## [54] "48\t1\t0.0\t2\t1"
## [55] "59\t1\t0.0\t2\t1"
## [56] "64\t1\t0.0\t2\t1"
## [57] ""
## [58] ""
## [59] "=== Second read: Adapter 3 ==="
## [60] ""
## [61] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [62] ""
## [63] "=== Second read: Adapter 4 ==="
## [64] ""
## [65] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 146 times"
## [66] ""
## [67] "No. of allowed errors:"
## [68] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [69] ""
## [70] "Bases preceding removed adapters:"
## [71] " A: 54.1%"
## [72] " C: 39.0%"
## [73] " G: 4.8%"
## [74] " T: 2.1%"
## [75] " none/other: 0.0%"
## [76] ""
## [77] "Overview of removed sequences"
## [78] "length\tcount\texpect\tmax.err\terror counts"
## [79] "5\t1\t3.1\t0\t1"
## [80] "8\t2\t0.0\t0\t2"
## [81] "9\t1\t0.0\t0\t1"
## [82] "10\t2\t0.0\t1\t2"
## [83] "12\t3\t0.0\t1\t3"
## [84] "14\t1\t0.0\t1\t1"
## [85] "15\t1\t0.0\t1\t1"
## [86] "16\t2\t0.0\t1\t2"
## [87] "20\t1\t0.0\t2\t1"
## [88] "21\t1\t0.0\t2\t1"
## [89] "22\t3\t0.0\t2\t1 2"
## [90] "23\t5\t0.0\t2\t5"
## [91] "24\t1\t0.0\t2\t0 1"
## [92] "25\t2\t0.0\t2\t2"
## [93] "27\t2\t0.0\t2\t2"
## [94] "28\t2\t0.0\t2\t2"
## [95] "30\t1\t0.0\t3\t1"
## [96] "33\t3\t0.0\t3\t1 2"
## [97] "34\t1\t0.0\t3\t1"
## [98] "36\t1\t0.0\t3\t0 1"
## [99] "37\t1\t0.0\t3\t1"
## [100] "39\t1\t0.0\t3\t1"
## [101] "41\t2\t0.0\t4\t1 1"
## [102] "42\t1\t0.0\t4\t1"
## [103] "43\t1\t0.0\t4\t0 1"
## [104] "44\t3\t0.0\t4\t2 1"
## [105] "45\t1\t0.0\t4\t1"
## [106] "48\t2\t0.0\t4\t1 1"
## [107] "49\t1\t0.0\t4\t1"
## [108] "50\t2\t0.0\t4\t2"
## [109] "52\t4\t0.0\t4\t4"
## [110] "55\t1\t0.0\t4\t1"
## [111] "56\t1\t0.0\t4\t1"
## [112] "57\t1\t0.0\t4\t1"
## [113] "60\t1\t0.0\t4\t0 0 1"
## [114] "61\t3\t0.0\t4\t2 1"
## [115] "63\t2\t0.0\t4\t2"
## [116] "64\t7\t0.0\t4\t6 1"
## [117] "65\t1\t0.0\t4\t1"
## [118] "66\t3\t0.0\t4\t2 0 1"
## [119] "67\t1\t0.0\t4\t0 1"
## [120] "68\t1\t0.0\t4\t1"
## [121] "69\t1\t0.0\t4\t0 1"
## [122] "72\t1\t0.0\t4\t1"
## [123] "74\t1\t0.0\t4\t1"
## [124] "75\t2\t0.0\t4\t2"
## [125] "76\t1\t0.0\t4\t1"
## [126] "77\t1\t0.0\t4\t1"
## [127] "78\t1\t0.0\t4\t0 1"
## [128] "80\t1\t0.0\t4\t1"
## [129] "81\t3\t0.0\t4\t1 1 1"
## [130] "82\t1\t0.0\t4\t1"
## [131] "83\t1\t0.0\t4\t1"
## [132] "84\t2\t0.0\t4\t2"
## [133] "86\t4\t0.0\t4\t3 1"
## [134] "87\t3\t0.0\t4\t2 1"
## [135] "88\t2\t0.0\t4\t2"
## [136] "89\t1\t0.0\t4\t1"
## [137] "91\t1\t0.0\t4\t1"
## [138] "92\t3\t0.0\t4\t3"
## [139] "93\t1\t0.0\t4\t1"
## [140] "94\t4\t0.0\t4\t4"
## [141] "95\t1\t0.0\t4\t1"
## [142] "96\t3\t0.0\t4\t2 1"
## [143] "98\t1\t0.0\t4\t1"
## [144] "104\t3\t0.0\t4\t3"
## [145] "105\t1\t0.0\t4\t1"
## [146] "106\t1\t0.0\t4\t1"
## [147] "108\t2\t0.0\t4\t2"
## [148] "110\t1\t0.0\t4\t0 0 0 1"
## [149] "111\t1\t0.0\t4\t1"
## [150] "112\t1\t0.0\t4\t1"
## [151] "113\t2\t0.0\t4\t2"
## [152] "116\t1\t0.0\t4\t1"
## [153] "119\t1\t0.0\t4\t1"
## [154] "120\t1\t0.0\t4\t0 1"
## [155] "127\t1\t0.0\t4\t1"
## [156] "130\t1\t0.0\t4\t1"
## [157] "134\t1\t0.0\t4\t1"
## [158] "140\t2\t0.0\t4\t2"
## [159] "141\t1\t0.0\t4\t1"
## [160] "146\t2\t0.0\t4\t2"
## [161] "147\t1\t0.0\t4\t1"
## [162] "148\t1\t0.0\t4\t1"
## [163] "162\t1\t0.0\t4\t1"
## [164] "170\t1\t0.0\t4\t1"
## [165] "177\t1\t0.0\t4\t1"
## [166] "186\t1\t0.0\t4\t1"
##
## [[38]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/188RNA3_S38_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/188RNA3_S38_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/188RNA3_S38_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/188RNA3_S38_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.49 s (126 us/read; 0.47 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 3,881"
## [9] " Read 1 with adapter: 102 (2.6%)"
## [10] " Read 2 with adapter: 265 (6.8%)"
## [11] "Pairs written (passing filters): 3,880 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 1,630,020 bp"
## [14] " Read 1: 760,676 bp"
## [15] " Read 2: 869,344 bp"
## [16] "Total written (filtered): 1,608,990 bp (98.7%)"
## [17] " Read 1: 757,923 bp"
## [18] " Read 2: 851,067 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 89 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "7\t1\t0.2\t0\t1"
## [30] "8\t2\t0.1\t0\t2"
## [31] "13\t1\t0.0\t1\t1"
## [32] "16\t2\t0.0\t1\t1 1"
## [33] "17\t57\t0.0\t1\t56 1"
## [34] "25\t1\t0.0\t2\t1"
## [35] "26\t1\t0.0\t2\t1"
## [36] "27\t1\t0.0\t2\t1"
## [37] "28\t6\t0.0\t2\t5 1"
## [38] "31\t14\t0.0\t3\t10 4"
## [39] "32\t1\t0.0\t3\t0 1"
## [40] "33\t1\t0.0\t3\t0 1"
## [41] "48\t1\t0.0\t4\t0 0 1"
## [42] ""
## [43] ""
## [44] "=== First read: Adapter 2 ==="
## [45] ""
## [46] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 13 times"
## [47] ""
## [48] "No. of allowed errors:"
## [49] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [50] ""
## [51] "Bases preceding removed adapters:"
## [52] " A: 30.8%"
## [53] " C: 7.7%"
## [54] " G: 46.2%"
## [55] " T: 15.4%"
## [56] " none/other: 0.0%"
## [57] ""
## [58] "Overview of removed sequences"
## [59] "length\tcount\texpect\tmax.err\terror counts"
## [60] "5\t1\t3.8\t0\t1"
## [61] "17\t2\t0.0\t1\t1 1"
## [62] "18\t1\t0.0\t1\t1"
## [63] "48\t1\t0.0\t2\t1"
## [64] "59\t1\t0.0\t2\t1"
## [65] "60\t1\t0.0\t2\t1"
## [66] "63\t1\t0.0\t2\t1"
## [67] "70\t1\t0.0\t2\t1"
## [68] "82\t1\t0.0\t2\t1"
## [69] "83\t1\t0.0\t2\t1"
## [70] "100\t1\t0.0\t2\t1"
## [71] "105\t1\t0.0\t2\t1"
## [72] ""
## [73] ""
## [74] "=== Second read: Adapter 3 ==="
## [75] ""
## [76] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 4 times"
## [77] ""
## [78] "No. of allowed errors:"
## [79] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [80] ""
## [81] "Overview of removed sequences"
## [82] "length\tcount\texpect\tmax.err\terror counts"
## [83] "17\t2\t0.0\t1\t2"
## [84] "27\t1\t0.0\t2\t1"
## [85] "30\t1\t0.0\t2\t0 1"
## [86] ""
## [87] ""
## [88] "=== Second read: Adapter 4 ==="
## [89] ""
## [90] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 261 times"
## [91] ""
## [92] "No. of allowed errors:"
## [93] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [94] ""
## [95] "Bases preceding removed adapters:"
## [96] " A: 64.8%"
## [97] " C: 26.8%"
## [98] " G: 1.9%"
## [99] " T: 6.5%"
## [100] " none/other: 0.0%"
## [101] ""
## [102] "Overview of removed sequences"
## [103] "length\tcount\texpect\tmax.err\terror counts"
## [104] "5\t4\t3.8\t0\t4"
## [105] "6\t1\t0.9\t0\t1"
## [106] "7\t1\t0.2\t0\t1"
## [107] "8\t2\t0.1\t0\t2"
## [108] "9\t1\t0.0\t0\t1"
## [109] "11\t1\t0.0\t1\t1"
## [110] "12\t2\t0.0\t1\t1 1"
## [111] "13\t1\t0.0\t1\t1"
## [112] "14\t4\t0.0\t1\t4"
## [113] "15\t3\t0.0\t1\t3"
## [114] "16\t1\t0.0\t1\t1"
## [115] "17\t1\t0.0\t1\t1"
## [116] "18\t3\t0.0\t1\t2 1"
## [117] "19\t1\t0.0\t1\t1"
## [118] "21\t1\t0.0\t2\t1"
## [119] "22\t2\t0.0\t2\t1 1"
## [120] "23\t4\t0.0\t2\t2 1 1"
## [121] "25\t6\t0.0\t2\t3 1 2"
## [122] "26\t1\t0.0\t2\t1"
## [123] "27\t4\t0.0\t2\t3 1"
## [124] "30\t4\t0.0\t3\t2 2"
## [125] "31\t2\t0.0\t3\t2"
## [126] "32\t2\t0.0\t3\t2"
## [127] "33\t4\t0.0\t3\t2 2"
## [128] "34\t1\t0.0\t3\t1"
## [129] "35\t4\t0.0\t3\t3 1"
## [130] "36\t1\t0.0\t3\t1"
## [131] "38\t2\t0.0\t3\t2"
## [132] "39\t2\t0.0\t3\t2"
## [133] "41\t3\t0.0\t4\t3"
## [134] "42\t5\t0.0\t4\t4 1"
## [135] "44\t1\t0.0\t4\t0 0 0 1"
## [136] "45\t6\t0.0\t4\t4 1 0 1"
## [137] "46\t6\t0.0\t4\t4 2"
## [138] "47\t1\t0.0\t4\t1"
## [139] "48\t2\t0.0\t4\t2"
## [140] "50\t2\t0.0\t4\t1 1"
## [141] "51\t3\t0.0\t4\t3"
## [142] "52\t6\t0.0\t4\t4 1 0 1"
## [143] "53\t4\t0.0\t4\t3 0 1"
## [144] "54\t3\t0.0\t4\t3"
## [145] "56\t2\t0.0\t4\t2"
## [146] "57\t3\t0.0\t4\t2 0 0 1"
## [147] "58\t3\t0.0\t4\t3"
## [148] "59\t1\t0.0\t4\t0 1"
## [149] "60\t1\t0.0\t4\t1"
## [150] "64\t2\t0.0\t4\t2"
## [151] "65\t1\t0.0\t4\t0 0 0 1"
## [152] "66\t1\t0.0\t4\t0 0 0 1"
## [153] "67\t6\t0.0\t4\t5 1"
## [154] "68\t1\t0.0\t4\t1"
## [155] "69\t2\t0.0\t4\t2"
## [156] "70\t1\t0.0\t4\t1"
## [157] "72\t1\t0.0\t4\t1"
## [158] "74\t3\t0.0\t4\t2 0 0 1"
## [159] "75\t6\t0.0\t4\t4 1 0 1"
## [160] "76\t6\t0.0\t4\t6"
## [161] "77\t3\t0.0\t4\t2 0 0 1"
## [162] "78\t2\t0.0\t4\t2"
## [163] "79\t4\t0.0\t4\t3 1"
## [164] "80\t1\t0.0\t4\t1"
## [165] "81\t2\t0.0\t4\t1 1"
## [166] "82\t1\t0.0\t4\t1"
## [167] "83\t4\t0.0\t4\t4"
## [168] "84\t1\t0.0\t4\t0 1"
## [169] "85\t4\t0.0\t4\t3 0 1"
## [170] "86\t4\t0.0\t4\t4"
## [171] "87\t2\t0.0\t4\t2"
## [172] "88\t3\t0.0\t4\t2 0 1"
## [173] "90\t3\t0.0\t4\t3"
## [174] "91\t1\t0.0\t4\t1"
## [175] "92\t4\t0.0\t4\t4"
## [176] "93\t2\t0.0\t4\t2"
## [177] "94\t6\t0.0\t4\t4 0 0 1 1"
## [178] "95\t2\t0.0\t4\t0 2"
## [179] "96\t3\t0.0\t4\t1 1 0 1"
## [180] "98\t2\t0.0\t4\t2"
## [181] "99\t1\t0.0\t4\t1"
## [182] "100\t2\t0.0\t4\t2"
## [183] "101\t4\t0.0\t4\t4"
## [184] "102\t1\t0.0\t4\t0 0 0 1"
## [185] "104\t3\t0.0\t4\t1 2"
## [186] "105\t1\t0.0\t4\t1"
## [187] "107\t2\t0.0\t4\t1 0 0 1"
## [188] "108\t2\t0.0\t4\t1 1"
## [189] "110\t3\t0.0\t4\t3"
## [190] "111\t2\t0.0\t4\t2"
## [191] "112\t3\t0.0\t4\t3"
## [192] "113\t2\t0.0\t4\t1 1"
## [193] "115\t2\t0.0\t4\t1 1"
## [194] "116\t3\t0.0\t4\t1 1 1"
## [195] "117\t1\t0.0\t4\t1"
## [196] "119\t1\t0.0\t4\t1"
## [197] "121\t4\t0.0\t4\t3 1"
## [198] "122\t1\t0.0\t4\t1"
## [199] "128\t2\t0.0\t4\t2"
## [200] "129\t1\t0.0\t4\t0 0 0 1"
## [201] "130\t1\t0.0\t4\t1"
## [202] "132\t1\t0.0\t4\t1"
## [203] "133\t1\t0.0\t4\t1"
## [204] "134\t2\t0.0\t4\t2"
## [205] "135\t1\t0.0\t4\t1"
## [206] "139\t1\t0.0\t4\t1"
## [207] "141\t1\t0.0\t4\t0 0 0 1"
## [208] "142\t1\t0.0\t4\t1"
## [209] "143\t1\t0.0\t4\t0 0 0 1"
## [210] "144\t1\t0.0\t4\t1"
## [211] "146\t1\t0.0\t4\t1"
## [212] "147\t1\t0.0\t4\t1"
## [213] "158\t1\t0.0\t4\t1"
## [214] "162\t1\t0.0\t4\t0 1"
## [215] "167\t1\t0.0\t4\t0 0 0 1"
## [216] "172\t1\t0.0\t4\t1"
## [217] "186\t1\t0.0\t4\t1"
##
## [[39]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/188RNA4_S39_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/188RNA4_S39_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/188RNA4_S39_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/188RNA4_S39_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.52 s (125 us/read; 0.48 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 4,143"
## [9] " Read 1 with adapter: 68 (1.6%)"
## [10] " Read 2 with adapter: 181 (4.4%)"
## [11] "Pairs written (passing filters): 4,142 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 1,740,060 bp"
## [14] " Read 1: 812,028 bp"
## [15] " Read 2: 928,032 bp"
## [16] "Total written (filtered): 1,722,841 bp (99.0%)"
## [17] " Read 1: 809,080 bp"
## [18] " Read 2: 913,761 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 47 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "8\t1\t0.1\t0\t1"
## [30] "15\t1\t0.0\t1\t1"
## [31] "16\t1\t0.0\t1\t1"
## [32] "17\t27\t0.0\t1\t26 1"
## [33] "27\t1\t0.0\t2\t1"
## [34] "30\t1\t0.0\t3\t1"
## [35] "31\t10\t0.0\t3\t9 1"
## [36] "32\t1\t0.0\t3\t1"
## [37] "61\t1\t0.0\t4\t0 0 1"
## [38] "62\t1\t0.0\t4\t0 1"
## [39] "63\t1\t0.0\t4\t0 0 1"
## [40] "79\t1\t0.0\t4\t0 0 1"
## [41] ""
## [42] ""
## [43] "=== First read: Adapter 2 ==="
## [44] ""
## [45] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 21 times"
## [46] ""
## [47] "No. of allowed errors:"
## [48] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [49] ""
## [50] "Bases preceding removed adapters:"
## [51] " A: 57.1%"
## [52] " C: 4.8%"
## [53] " G: 38.1%"
## [54] " T: 0.0%"
## [55] " none/other: 0.0%"
## [56] ""
## [57] "Overview of removed sequences"
## [58] "length\tcount\texpect\tmax.err\terror counts"
## [59] "16\t2\t0.0\t1\t2"
## [60] "17\t1\t0.0\t1\t1"
## [61] "18\t1\t0.0\t1\t1"
## [62] "49\t1\t0.0\t2\t1"
## [63] "59\t2\t0.0\t2\t2"
## [64] "66\t2\t0.0\t2\t2"
## [65] "71\t1\t0.0\t2\t1"
## [66] "74\t2\t0.0\t2\t2"
## [67] "82\t1\t0.0\t2\t1"
## [68] "90\t1\t0.0\t2\t1"
## [69] "101\t1\t0.0\t2\t1"
## [70] "102\t1\t0.0\t2\t1"
## [71] "118\t1\t0.0\t2\t1"
## [72] "122\t2\t0.0\t2\t2"
## [73] "125\t1\t0.0\t2\t1"
## [74] "143\t1\t0.0\t2\t1"
## [75] ""
## [76] ""
## [77] "=== Second read: Adapter 3 ==="
## [78] ""
## [79] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 3 times"
## [80] ""
## [81] "No. of allowed errors:"
## [82] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [83] ""
## [84] "Overview of removed sequences"
## [85] "length\tcount\texpect\tmax.err\terror counts"
## [86] "18\t1\t0.0\t1\t1"
## [87] "30\t1\t0.0\t2\t1"
## [88] "48\t1\t0.0\t2\t1"
## [89] ""
## [90] ""
## [91] "=== Second read: Adapter 4 ==="
## [92] ""
## [93] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 178 times"
## [94] ""
## [95] "No. of allowed errors:"
## [96] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [97] ""
## [98] "Bases preceding removed adapters:"
## [99] " A: 74.2%"
## [100] " C: 19.1%"
## [101] " G: 3.9%"
## [102] " T: 2.8%"
## [103] " none/other: 0.0%"
## [104] ""
## [105] "Overview of removed sequences"
## [106] "length\tcount\texpect\tmax.err\terror counts"
## [107] "5\t2\t4.0\t0\t2"
## [108] "6\t1\t1.0\t0\t1"
## [109] "16\t4\t0.0\t1\t4"
## [110] "17\t1\t0.0\t1\t0 1"
## [111] "20\t1\t0.0\t2\t0 0 1"
## [112] "22\t2\t0.0\t2\t2"
## [113] "23\t1\t0.0\t2\t1"
## [114] "24\t1\t0.0\t2\t1"
## [115] "25\t9\t0.0\t2\t8 1"
## [116] "27\t1\t0.0\t2\t0 0 1"
## [117] "31\t3\t0.0\t3\t2 0 1"
## [118] "33\t1\t0.0\t3\t0 1"
## [119] "35\t2\t0.0\t3\t2"
## [120] "37\t1\t0.0\t3\t1"
## [121] "39\t2\t0.0\t3\t1 1"
## [122] "41\t1\t0.0\t4\t1"
## [123] "42\t3\t0.0\t4\t3"
## [124] "43\t3\t0.0\t4\t2 0 0 1"
## [125] "44\t3\t0.0\t4\t3"
## [126] "45\t5\t0.0\t4\t3 1 1"
## [127] "46\t3\t0.0\t4\t2 1"
## [128] "47\t1\t0.0\t4\t1"
## [129] "49\t1\t0.0\t4\t0 0 1"
## [130] "50\t3\t0.0\t4\t3"
## [131] "51\t1\t0.0\t4\t1"
## [132] "52\t4\t0.0\t4\t1 1 0 1 1"
## [133] "53\t1\t0.0\t4\t0 0 0 1"
## [134] "54\t1\t0.0\t4\t0 0 0 1"
## [135] "57\t1\t0.0\t4\t1"
## [136] "58\t2\t0.0\t4\t1 0 0 1"
## [137] "59\t3\t0.0\t4\t2 0 0 1"
## [138] "63\t1\t0.0\t4\t1"
## [139] "65\t1\t0.0\t4\t1"
## [140] "67\t1\t0.0\t4\t1"
## [141] "69\t1\t0.0\t4\t1"
## [142] "70\t1\t0.0\t4\t0 0 0 1"
## [143] "72\t1\t0.0\t4\t0 0 1"
## [144] "73\t1\t0.0\t4\t1"
## [145] "74\t1\t0.0\t4\t1"
## [146] "75\t1\t0.0\t4\t0 1"
## [147] "76\t2\t0.0\t4\t1 1"
## [148] "77\t3\t0.0\t4\t2 1"
## [149] "78\t4\t0.0\t4\t3 0 0 1"
## [150] "79\t2\t0.0\t4\t2"
## [151] "82\t1\t0.0\t4\t1"
## [152] "84\t2\t0.0\t4\t2"
## [153] "86\t3\t0.0\t4\t3"
## [154] "87\t4\t0.0\t4\t4"
## [155] "88\t1\t0.0\t4\t1"
## [156] "89\t1\t0.0\t4\t1"
## [157] "90\t1\t0.0\t4\t1"
## [158] "91\t1\t0.0\t4\t1"
## [159] "92\t2\t0.0\t4\t2"
## [160] "93\t6\t0.0\t4\t6"
## [161] "94\t9\t0.0\t4\t8 1"
## [162] "95\t1\t0.0\t4\t0 0 0 1"
## [163] "96\t1\t0.0\t4\t0 0 0 1"
## [164] "97\t1\t0.0\t4\t0 1"
## [165] "99\t1\t0.0\t4\t0 1"
## [166] "100\t1\t0.0\t4\t1"
## [167] "101\t2\t0.0\t4\t1 0 1"
## [168] "102\t3\t0.0\t4\t2 0 0 1"
## [169] "103\t3\t0.0\t4\t3"
## [170] "104\t4\t0.0\t4\t3 0 0 1"
## [171] "105\t2\t0.0\t4\t2"
## [172] "106\t1\t0.0\t4\t0 0 0 0 1"
## [173] "107\t1\t0.0\t4\t1"
## [174] "109\t1\t0.0\t4\t1"
## [175] "111\t1\t0.0\t4\t0 0 0 1"
## [176] "112\t3\t0.0\t4\t2 0 0 1"
## [177] "113\t1\t0.0\t4\t1"
## [178] "115\t2\t0.0\t4\t1 1"
## [179] "118\t1\t0.0\t4\t1"
## [180] "120\t1\t0.0\t4\t1"
## [181] "121\t1\t0.0\t4\t1"
## [182] "125\t2\t0.0\t4\t2"
## [183] "126\t1\t0.0\t4\t1"
## [184] "127\t1\t0.0\t4\t1"
## [185] "129\t3\t0.0\t4\t2 0 1"
## [186] "130\t1\t0.0\t4\t1"
## [187] "138\t1\t0.0\t4\t1"
## [188] "140\t2\t0.0\t4\t2"
## [189] "143\t1\t0.0\t4\t1"
## [190] "144\t1\t0.0\t4\t0 0 0 1"
## [191] "146\t1\t0.0\t4\t1"
## [192] "147\t2\t0.0\t4\t2"
## [193] "150\t2\t0.0\t4\t2"
## [194] "151\t2\t0.0\t4\t1 1"
## [195] "153\t1\t0.0\t4\t1"
## [196] "159\t1\t0.0\t4\t1"
## [197] "160\t2\t0.0\t4\t2"
## [198] "171\t1\t0.0\t4\t1"
## [199] "173\t1\t0.0\t4\t0 0 0 1"
## [200] "175\t1\t0.0\t4\t1"
##
## [[40]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/188RNA5_S40_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/188RNA5_S40_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/188RNA5_S40_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/188RNA5_S40_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.62 s (124 us/read; 0.48 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 5,004"
## [9] " Read 1 with adapter: 72 (1.4%)"
## [10] " Read 2 with adapter: 196 (3.9%)"
## [11] "Pairs written (passing filters): 5,003 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 2,101,680 bp"
## [14] " Read 1: 980,784 bp"
## [15] " Read 2: 1,120,896 bp"
## [16] "Total written (filtered): 2,081,169 bp (99.0%)"
## [17] " Read 1: 975,805 bp"
## [18] " Read 2: 1,105,364 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 2 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t4.9\t0\t1"
## [30] "30\t1\t0.0\t3\t1"
## [31] ""
## [32] ""
## [33] "=== First read: Adapter 2 ==="
## [34] ""
## [35] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 70 times"
## [36] ""
## [37] "No. of allowed errors:"
## [38] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [39] ""
## [40] "Bases preceding removed adapters:"
## [41] " A: 20.0%"
## [42] " C: 1.4%"
## [43] " G: 65.7%"
## [44] " T: 12.9%"
## [45] " none/other: 0.0%"
## [46] ""
## [47] "Overview of removed sequences"
## [48] "length\tcount\texpect\tmax.err\terror counts"
## [49] "5\t1\t4.9\t0\t1"
## [50] "12\t1\t0.0\t1\t1"
## [51] "16\t3\t0.0\t1\t3"
## [52] "17\t1\t0.0\t1\t1"
## [53] "26\t1\t0.0\t2\t1"
## [54] "35\t1\t0.0\t2\t1"
## [55] "36\t9\t0.0\t2\t9"
## [56] "37\t2\t0.0\t2\t2"
## [57] "41\t1\t0.0\t2\t1"
## [58] "45\t1\t0.0\t2\t1"
## [59] "55\t3\t0.0\t2\t2 0 1"
## [60] "56\t2\t0.0\t2\t1 1"
## [61] "59\t1\t0.0\t2\t1"
## [62] "60\t2\t0.0\t2\t2"
## [63] "61\t1\t0.0\t2\t1"
## [64] "62\t1\t0.0\t2\t1"
## [65] "72\t5\t0.0\t2\t5"
## [66] "74\t2\t0.0\t2\t2"
## [67] "75\t5\t0.0\t2\t5"
## [68] "76\t2\t0.0\t2\t2"
## [69] "79\t1\t0.0\t2\t1"
## [70] "82\t7\t0.0\t2\t7"
## [71] "90\t7\t0.0\t2\t7"
## [72] "93\t1\t0.0\t2\t1"
## [73] "103\t1\t0.0\t2\t1"
## [74] "106\t2\t0.0\t2\t2"
## [75] "122\t1\t0.0\t2\t1"
## [76] "132\t1\t0.0\t2\t1"
## [77] "136\t1\t0.0\t2\t1"
## [78] "142\t3\t0.0\t2\t3"
## [79] ""
## [80] ""
## [81] "=== Second read: Adapter 3 ==="
## [82] ""
## [83] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [84] ""
## [85] "=== Second read: Adapter 4 ==="
## [86] ""
## [87] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 196 times"
## [88] ""
## [89] "No. of allowed errors:"
## [90] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [91] ""
## [92] "Bases preceding removed adapters:"
## [93] " A: 76.0%"
## [94] " C: 16.8%"
## [95] " G: 3.6%"
## [96] " T: 3.6%"
## [97] " none/other: 0.0%"
## [98] ""
## [99] "Overview of removed sequences"
## [100] "length\tcount\texpect\tmax.err\terror counts"
## [101] "5\t4\t4.9\t0\t4"
## [102] "6\t2\t1.2\t0\t2"
## [103] "8\t1\t0.1\t0\t1"
## [104] "9\t1\t0.0\t0\t1"
## [105] "11\t1\t0.0\t1\t1"
## [106] "12\t1\t0.0\t1\t0 1"
## [107] "14\t2\t0.0\t1\t2"
## [108] "16\t6\t0.0\t1\t5 1"
## [109] "17\t1\t0.0\t1\t1"
## [110] "20\t2\t0.0\t2\t1 1"
## [111] "21\t1\t0.0\t2\t1"
## [112] "22\t2\t0.0\t2\t2"
## [113] "23\t1\t0.0\t2\t1"
## [114] "26\t1\t0.0\t2\t1"
## [115] "30\t2\t0.0\t3\t1 1"
## [116] "32\t4\t0.0\t3\t3 0 1"
## [117] "33\t3\t0.0\t3\t3"
## [118] "35\t2\t0.0\t3\t1 1"
## [119] "36\t1\t0.0\t3\t1"
## [120] "39\t1\t0.0\t3\t1"
## [121] "40\t1\t0.0\t4\t1"
## [122] "42\t1\t0.0\t4\t1"
## [123] "43\t3\t0.0\t4\t3"
## [124] "44\t5\t0.0\t4\t3 2"
## [125] "45\t1\t0.0\t4\t0 1"
## [126] "47\t1\t0.0\t4\t1"
## [127] "49\t1\t0.0\t4\t1"
## [128] "51\t1\t0.0\t4\t1"
## [129] "52\t3\t0.0\t4\t3"
## [130] "53\t1\t0.0\t4\t1"
## [131] "54\t1\t0.0\t4\t1"
## [132] "56\t1\t0.0\t4\t1"
## [133] "58\t2\t0.0\t4\t2"
## [134] "62\t1\t0.0\t4\t1"
## [135] "63\t1\t0.0\t4\t1"
## [136] "64\t12\t0.0\t4\t10 2"
## [137] "65\t1\t0.0\t4\t1"
## [138] "66\t1\t0.0\t4\t1"
## [139] "68\t1\t0.0\t4\t1"
## [140] "69\t1\t0.0\t4\t1"
## [141] "73\t5\t0.0\t4\t3 1 0 0 1"
## [142] "74\t1\t0.0\t4\t1"
## [143] "75\t3\t0.0\t4\t2 1"
## [144] "76\t2\t0.0\t4\t2"
## [145] "77\t3\t0.0\t4\t3"
## [146] "78\t1\t0.0\t4\t1"
## [147] "80\t2\t0.0\t4\t1 1"
## [148] "83\t3\t0.0\t4\t3"
## [149] "84\t2\t0.0\t4\t1 0 0 1"
## [150] "85\t3\t0.0\t4\t2 0 0 1"
## [151] "86\t3\t0.0\t4\t2 1"
## [152] "87\t3\t0.0\t4\t3"
## [153] "88\t2\t0.0\t4\t2"
## [154] "89\t2\t0.0\t4\t1 0 0 1"
## [155] "90\t1\t0.0\t4\t1"
## [156] "94\t1\t0.0\t4\t1"
## [157] "95\t4\t0.0\t4\t3 1"
## [158] "96\t1\t0.0\t4\t1"
## [159] "97\t1\t0.0\t4\t1"
## [160] "99\t1\t0.0\t4\t0 1"
## [161] "100\t6\t0.0\t4\t4 2"
## [162] "101\t2\t0.0\t4\t1 1"
## [163] "102\t3\t0.0\t4\t3"
## [164] "103\t9\t0.0\t4\t6 3"
## [165] "104\t2\t0.0\t4\t2"
## [166] "105\t1\t0.0\t4\t1"
## [167] "106\t3\t0.0\t4\t2 1"
## [168] "107\t1\t0.0\t4\t1"
## [169] "108\t1\t0.0\t4\t1"
## [170] "109\t1\t0.0\t4\t0 1"
## [171] "110\t8\t0.0\t4\t8"
## [172] "114\t1\t0.0\t4\t0 1"
## [173] "115\t1\t0.0\t4\t1"
## [174] "117\t1\t0.0\t4\t1"
## [175] "118\t8\t0.0\t4\t7 0 1"
## [176] "119\t2\t0.0\t4\t2"
## [177] "120\t1\t0.0\t4\t1"
## [178] "127\t2\t0.0\t4\t2"
## [179] "130\t1\t0.0\t4\t1"
## [180] "131\t2\t0.0\t4\t2"
## [181] "132\t1\t0.0\t4\t0 1"
## [182] "134\t2\t0.0\t4\t2"
## [183] "135\t1\t0.0\t4\t1"
## [184] "142\t1\t0.0\t4\t0 1"
## [185] "148\t1\t0.0\t4\t1"
## [186] "149\t1\t0.0\t4\t1"
## [187] "150\t1\t0.0\t4\t1"
## [188] "155\t1\t0.0\t4\t1"
## [189] "156\t1\t0.0\t4\t1"
## [190] "160\t1\t0.0\t4\t0 0 0 0 1"
## [191] "164\t1\t0.0\t4\t1"
## [192] "170\t3\t0.0\t4\t3"
## [193] "171\t1\t0.0\t4\t1"
## [194] "175\t1\t0.0\t4\t1"
##
## [[41]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/188RNA6_S41_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/188RNA6_S41_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/188RNA6_S41_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/188RNA6_S41_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.20 s (117 us/read; 0.51 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 10,268"
## [9] " Read 1 with adapter: 41 (0.4%)"
## [10] " Read 2 with adapter: 181 (1.8%)"
## [11] "Pairs written (passing filters): 10,267 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 4,312,560 bp"
## [14] " Read 1: 2,012,528 bp"
## [15] " Read 2: 2,300,032 bp"
## [16] "Total written (filtered): 4,298,819 bp (99.7%)"
## [17] " Read 1: 2,010,217 bp"
## [18] " Read 2: 2,288,602 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "22\t1\t0.0\t2\t1"
## [30] "29\t1\t0.0\t2\t1"
## [31] "32\t1\t0.0\t3\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 38 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 31.6%"
## [43] " C: 2.6%"
## [44] " G: 63.2%"
## [45] " T: 2.6%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "8\t2\t0.2\t0\t2"
## [51] "10\t1\t0.0\t1\t1"
## [52] "15\t1\t0.0\t1\t1"
## [53] "17\t3\t0.0\t1\t3"
## [54] "18\t2\t0.0\t1\t2"
## [55] "28\t1\t0.0\t2\t1"
## [56] "36\t5\t0.0\t2\t5"
## [57] "39\t1\t0.0\t2\t0 1"
## [58] "45\t1\t0.0\t2\t1"
## [59] "47\t3\t0.0\t2\t3"
## [60] "49\t2\t0.0\t2\t2"
## [61] "60\t1\t0.0\t2\t1"
## [62] "72\t1\t0.0\t2\t1"
## [63] "73\t1\t0.0\t2\t1"
## [64] "76\t1\t0.0\t2\t0 1"
## [65] "78\t1\t0.0\t2\t1"
## [66] "82\t1\t0.0\t2\t1"
## [67] "90\t7\t0.0\t2\t7"
## [68] "93\t1\t0.0\t2\t1"
## [69] "100\t1\t0.0\t2\t1"
## [70] "109\t1\t0.0\t2\t1"
## [71] ""
## [72] ""
## [73] "=== Second read: Adapter 3 ==="
## [74] ""
## [75] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [76] ""
## [77] "=== Second read: Adapter 4 ==="
## [78] ""
## [79] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 181 times"
## [80] ""
## [81] "No. of allowed errors:"
## [82] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [83] ""
## [84] "Bases preceding removed adapters:"
## [85] " A: 79.6%"
## [86] " C: 17.7%"
## [87] " G: 0.0%"
## [88] " T: 2.8%"
## [89] " none/other: 0.0%"
## [90] ""
## [91] "Overview of removed sequences"
## [92] "length\tcount\texpect\tmax.err\terror counts"
## [93] "5\t9\t10.0\t0\t9"
## [94] "6\t3\t2.5\t0\t3"
## [95] "8\t5\t0.2\t0\t5"
## [96] "9\t2\t0.0\t0\t2"
## [97] "12\t1\t0.0\t1\t1"
## [98] "13\t1\t0.0\t1\t0 1"
## [99] "14\t4\t0.0\t1\t4"
## [100] "15\t1\t0.0\t1\t1"
## [101] "16\t2\t0.0\t1\t1 1"
## [102] "17\t3\t0.0\t1\t3"
## [103] "19\t1\t0.0\t1\t1"
## [104] "20\t1\t0.0\t2\t0 1"
## [105] "22\t3\t0.0\t2\t3"
## [106] "23\t3\t0.0\t2\t3"
## [107] "24\t1\t0.0\t2\t0 1"
## [108] "25\t8\t0.0\t2\t7 0 1"
## [109] "27\t1\t0.0\t2\t1"
## [110] "29\t2\t0.0\t2\t1 1"
## [111] "30\t1\t0.0\t3\t1"
## [112] "31\t3\t0.0\t3\t1 1 1"
## [113] "33\t2\t0.0\t3\t2"
## [114] "34\t2\t0.0\t3\t2"
## [115] "35\t2\t0.0\t3\t2"
## [116] "36\t4\t0.0\t3\t1 2 1"
## [117] "38\t2\t0.0\t3\t0 2"
## [118] "40\t1\t0.0\t4\t0 1"
## [119] "41\t1\t0.0\t4\t1"
## [120] "43\t1\t0.0\t4\t0 0 0 0 1"
## [121] "44\t1\t0.0\t4\t1"
## [122] "45\t4\t0.0\t4\t2 1 1"
## [123] "46\t5\t0.0\t4\t5"
## [124] "47\t1\t0.0\t4\t1"
## [125] "48\t2\t0.0\t4\t2"
## [126] "51\t2\t0.0\t4\t2"
## [127] "52\t3\t0.0\t4\t2 0 0 1"
## [128] "56\t2\t0.0\t4\t1 0 0 1"
## [129] "57\t3\t0.0\t4\t2 1"
## [130] "58\t1\t0.0\t4\t1"
## [131] "63\t2\t0.0\t4\t2"
## [132] "64\t7\t0.0\t4\t7"
## [133] "67\t1\t0.0\t4\t1"
## [134] "69\t1\t0.0\t4\t1"
## [135] "73\t2\t0.0\t4\t1 1"
## [136] "74\t1\t0.0\t4\t1"
## [137] "75\t2\t0.0\t4\t1 1"
## [138] "76\t2\t0.0\t4\t1 0 0 0 1"
## [139] "77\t4\t0.0\t4\t3 1"
## [140] "78\t1\t0.0\t4\t1"
## [141] "79\t2\t0.0\t4\t2"
## [142] "80\t1\t0.0\t4\t1"
## [143] "83\t1\t0.0\t4\t0 1"
## [144] "85\t1\t0.0\t4\t1"
## [145] "86\t2\t0.0\t4\t2"
## [146] "88\t2\t0.0\t4\t1 1"
## [147] "89\t1\t0.0\t4\t1"
## [148] "91\t2\t0.0\t4\t2"
## [149] "92\t2\t0.0\t4\t2"
## [150] "93\t2\t0.0\t4\t2"
## [151] "94\t2\t0.0\t4\t2"
## [152] "95\t2\t0.0\t4\t1 1"
## [153] "96\t2\t0.0\t4\t2"
## [154] "98\t3\t0.0\t4\t3"
## [155] "100\t2\t0.0\t4\t2"
## [156] "101\t1\t0.0\t4\t1"
## [157] "103\t1\t0.0\t4\t1"
## [158] "104\t2\t0.0\t4\t2"
## [159] "105\t2\t0.0\t4\t2"
## [160] "106\t3\t0.0\t4\t3"
## [161] "107\t1\t0.0\t4\t1"
## [162] "110\t1\t0.0\t4\t1"
## [163] "116\t1\t0.0\t4\t1"
## [164] "117\t1\t0.0\t4\t0 1"
## [165] "118\t8\t0.0\t4\t8"
## [166] "121\t1\t0.0\t4\t1"
## [167] "127\t1\t0.0\t4\t1"
## [168] "128\t1\t0.0\t4\t1"
## [169] "129\t1\t0.0\t4\t1"
## [170] "132\t1\t0.0\t4\t1"
## [171] "133\t1\t0.0\t4\t1"
## [172] "137\t2\t0.0\t4\t2"
## [173] "144\t1\t0.0\t4\t1"
## [174] "148\t1\t0.0\t4\t1"
## [175] "152\t1\t0.0\t4\t1"
## [176] "158\t1\t0.0\t4\t1"
## [177] "160\t1\t0.0\t4\t1"
## [178] "166\t1\t0.0\t4\t1"
## [179] "173\t1\t0.0\t4\t1"
## [180] "189\t1\t0.0\t4\t1"
##
## [[42]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/188RNA7_S42_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/188RNA7_S42_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/188RNA7_S42_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/188RNA7_S42_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.29 s (120 us/read; 0.50 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 10,772"
## [9] " Read 1 with adapter: 53 (0.5%)"
## [10] " Read 2 with adapter: 241 (2.2%)"
## [11] "Pairs written (passing filters): 10,772 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 4,524,240 bp"
## [14] " Read 1: 2,111,312 bp"
## [15] " Read 2: 2,412,928 bp"
## [16] "Total written (filtered): 4,506,003 bp (99.6%)"
## [17] " Read 1: 2,108,699 bp"
## [18] " Read 2: 2,397,304 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "7\t1\t0.7\t0\t1"
## [30] "29\t1\t0.0\t2\t1"
## [31] "32\t1\t0.0\t3\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 50 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 16.0%"
## [43] " C: 6.0%"
## [44] " G: 72.0%"
## [45] " T: 6.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "5\t1\t10.5\t0\t1"
## [51] "6\t2\t2.6\t0\t2"
## [52] "9\t1\t0.0\t0\t0 1"
## [53] "15\t1\t0.0\t1\t1"
## [54] "17\t1\t0.0\t1\t1"
## [55] "36\t21\t0.0\t2\t20 1"
## [56] "38\t1\t0.0\t2\t1"
## [57] "41\t1\t0.0\t2\t1"
## [58] "44\t1\t0.0\t2\t1"
## [59] "60\t2\t0.0\t2\t2"
## [60] "70\t1\t0.0\t2\t1"
## [61] "71\t1\t0.0\t2\t1"
## [62] "73\t2\t0.0\t2\t2"
## [63] "74\t1\t0.0\t2\t1"
## [64] "75\t1\t0.0\t2\t1"
## [65] "82\t3\t0.0\t2\t3"
## [66] "83\t1\t0.0\t2\t1"
## [67] "89\t1\t0.0\t2\t1"
## [68] "90\t6\t0.0\t2\t6"
## [69] "94\t1\t0.0\t2\t1"
## [70] ""
## [71] ""
## [72] "=== Second read: Adapter 3 ==="
## [73] ""
## [74] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [75] ""
## [76] "No. of allowed errors:"
## [77] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [78] ""
## [79] "Overview of removed sequences"
## [80] "length\tcount\texpect\tmax.err\terror counts"
## [81] "100\t1\t0.0\t2\t0 0 1"
## [82] ""
## [83] ""
## [84] "=== Second read: Adapter 4 ==="
## [85] ""
## [86] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 240 times"
## [87] ""
## [88] "No. of allowed errors:"
## [89] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [90] ""
## [91] "Bases preceding removed adapters:"
## [92] " A: 82.1%"
## [93] " C: 15.0%"
## [94] " G: 1.2%"
## [95] " T: 1.7%"
## [96] " none/other: 0.0%"
## [97] "WARNING:"
## [98] " The adapter is preceded by \"A\" extremely often."
## [99] " The provided adapter sequence could be incomplete at its 3' end."
## [100] ""
## [101] "Overview of removed sequences"
## [102] "length\tcount\texpect\tmax.err\terror counts"
## [103] "5\t2\t10.5\t0\t2"
## [104] "6\t3\t2.6\t0\t3"
## [105] "8\t2\t0.2\t0\t2"
## [106] "9\t4\t0.0\t0\t4"
## [107] "11\t1\t0.0\t1\t1"
## [108] "12\t2\t0.0\t1\t2"
## [109] "13\t1\t0.0\t1\t1"
## [110] "14\t1\t0.0\t1\t1"
## [111] "15\t1\t0.0\t1\t1"
## [112] "16\t4\t0.0\t1\t4"
## [113] "17\t1\t0.0\t1\t1"
## [114] "20\t1\t0.0\t2\t1"
## [115] "22\t5\t0.0\t2\t2 2 1"
## [116] "23\t1\t0.0\t2\t1"
## [117] "24\t3\t0.0\t2\t2 1"
## [118] "25\t8\t0.0\t2\t5 3"
## [119] "26\t2\t0.0\t2\t2"
## [120] "27\t7\t0.0\t2\t7"
## [121] "28\t1\t0.0\t2\t1"
## [122] "29\t2\t0.0\t2\t2"
## [123] "30\t2\t0.0\t3\t2"
## [124] "31\t2\t0.0\t3\t2"
## [125] "32\t1\t0.0\t3\t1"
## [126] "33\t2\t0.0\t3\t1 0 1"
## [127] "34\t4\t0.0\t3\t3 1"
## [128] "35\t1\t0.0\t3\t0 1"
## [129] "36\t3\t0.0\t3\t3"
## [130] "37\t1\t0.0\t3\t0 0 1"
## [131] "38\t3\t0.0\t3\t2 1"
## [132] "39\t1\t0.0\t3\t0 1"
## [133] "40\t1\t0.0\t4\t1"
## [134] "41\t3\t0.0\t4\t3"
## [135] "43\t2\t0.0\t4\t2"
## [136] "44\t2\t0.0\t4\t2"
## [137] "45\t4\t0.0\t4\t3 1"
## [138] "46\t6\t0.0\t4\t4 2"
## [139] "47\t2\t0.0\t4\t2"
## [140] "48\t2\t0.0\t4\t1 0 1"
## [141] "49\t1\t0.0\t4\t1"
## [142] "50\t1\t0.0\t4\t1"
## [143] "52\t5\t0.0\t4\t5"
## [144] "53\t2\t0.0\t4\t2"
## [145] "54\t1\t0.0\t4\t1"
## [146] "57\t1\t0.0\t4\t1"
## [147] "58\t1\t0.0\t4\t1"
## [148] "59\t1\t0.0\t4\t1"
## [149] "60\t2\t0.0\t4\t2"
## [150] "62\t3\t0.0\t4\t3"
## [151] "63\t2\t0.0\t4\t2"
## [152] "64\t25\t0.0\t4\t21 4"
## [153] "65\t1\t0.0\t4\t1"
## [154] "66\t3\t0.0\t4\t2 1"
## [155] "67\t1\t0.0\t4\t1"
## [156] "68\t1\t0.0\t4\t1"
## [157] "69\t1\t0.0\t4\t1"
## [158] "70\t1\t0.0\t4\t1"
## [159] "72\t2\t0.0\t4\t1 1"
## [160] "74\t3\t0.0\t4\t3"
## [161] "75\t4\t0.0\t4\t3 1"
## [162] "76\t1\t0.0\t4\t1"
## [163] "79\t2\t0.0\t4\t2"
## [164] "81\t1\t0.0\t4\t1"
## [165] "82\t1\t0.0\t4\t1"
## [166] "83\t1\t0.0\t4\t0 1"
## [167] "84\t3\t0.0\t4\t3"
## [168] "85\t1\t0.0\t4\t1"
## [169] "86\t4\t0.0\t4\t4"
## [170] "88\t2\t0.0\t4\t2"
## [171] "89\t3\t0.0\t4\t2 0 0 1"
## [172] "91\t1\t0.0\t4\t1"
## [173] "92\t1\t0.0\t4\t1"
## [174] "93\t3\t0.0\t4\t2 1"
## [175] "94\t2\t0.0\t4\t2"
## [176] "97\t1\t0.0\t4\t1"
## [177] "98\t2\t0.0\t4\t2"
## [178] "99\t1\t0.0\t4\t1"
## [179] "100\t2\t0.0\t4\t2"
## [180] "101\t3\t0.0\t4\t2 1"
## [181] "102\t3\t0.0\t4\t2 1"
## [182] "103\t3\t0.0\t4\t3"
## [183] "104\t4\t0.0\t4\t3 1"
## [184] "105\t3\t0.0\t4\t3"
## [185] "106\t1\t0.0\t4\t1"
## [186] "108\t3\t0.0\t4\t3"
## [187] "109\t1\t0.0\t4\t1"
## [188] "110\t6\t0.0\t4\t5 1"
## [189] "115\t2\t0.0\t4\t2"
## [190] "117\t2\t0.0\t4\t2"
## [191] "118\t6\t0.0\t4\t6"
## [192] "122\t1\t0.0\t4\t1"
## [193] "123\t2\t0.0\t4\t2"
## [194] "125\t1\t0.0\t4\t1"
## [195] "127\t2\t0.0\t4\t2"
## [196] "131\t1\t0.0\t4\t1"
## [197] "132\t1\t0.0\t4\t1"
## [198] "144\t1\t0.0\t4\t1"
## [199] "145\t1\t0.0\t4\t1"
## [200] "146\t1\t0.0\t4\t1"
## [201] "150\t1\t0.0\t4\t1"
## [202] "153\t1\t0.0\t4\t1"
## [203] "155\t1\t0.0\t4\t1"
## [204] "165\t1\t0.0\t4\t1"
## [205] ""
## [206] ""
## [207] "WARNING:"
## [208] " One or more of your adapter sequences may be incomplete."
## [209] " Please see the detailed output above."
##
## [[43]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/41_S43_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/41_S43_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/41_S43_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/41_S43_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.00 s (112 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 8,960"
## [9] " Read 1 with adapter: 7 (0.1%)"
## [10] " Read 2 with adapter: 157 (1.8%)"
## [11] "Pairs written (passing filters): 8,960 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,763,200 bp"
## [14] " Read 1: 1,756,160 bp"
## [15] " Read 2: 2,007,040 bp"
## [16] "Total written (filtered): 3,753,175 bp (99.7%)"
## [17] " Read 1: 1,755,805 bp"
## [18] " Read 2: 1,997,370 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 2 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "9\t1\t0.0\t0\t1"
## [30] "17\t1\t0.0\t1\t1"
## [31] ""
## [32] ""
## [33] "=== First read: Adapter 2 ==="
## [34] ""
## [35] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 5 times"
## [36] ""
## [37] "No. of allowed errors:"
## [38] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [39] ""
## [40] "Bases preceding removed adapters:"
## [41] " A: 0.0%"
## [42] " C: 0.0%"
## [43] " G: 80.0%"
## [44] " T: 20.0%"
## [45] " none/other: 0.0%"
## [46] ""
## [47] "Overview of removed sequences"
## [48] "length\tcount\texpect\tmax.err\terror counts"
## [49] "5\t2\t8.8\t0\t2"
## [50] "86\t1\t0.0\t2\t1"
## [51] "96\t1\t0.0\t2\t1"
## [52] "137\t1\t0.0\t2\t1"
## [53] ""
## [54] ""
## [55] "=== Second read: Adapter 3 ==="
## [56] ""
## [57] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [58] ""
## [59] "No. of allowed errors:"
## [60] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [61] ""
## [62] "Overview of removed sequences"
## [63] "length\tcount\texpect\tmax.err\terror counts"
## [64] "9\t1\t0.0\t0\t1"
## [65] ""
## [66] ""
## [67] "=== Second read: Adapter 4 ==="
## [68] ""
## [69] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 156 times"
## [70] ""
## [71] "No. of allowed errors:"
## [72] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [73] ""
## [74] "Bases preceding removed adapters:"
## [75] " A: 84.6%"
## [76] " C: 9.6%"
## [77] " G: 1.3%"
## [78] " T: 4.5%"
## [79] " none/other: 0.0%"
## [80] "WARNING:"
## [81] " The adapter is preceded by \"A\" extremely often."
## [82] " The provided adapter sequence could be incomplete at its 3' end."
## [83] ""
## [84] "Overview of removed sequences"
## [85] "length\tcount\texpect\tmax.err\terror counts"
## [86] "5\t4\t8.8\t0\t4"
## [87] "6\t1\t2.2\t0\t1"
## [88] "8\t5\t0.1\t0\t5"
## [89] "9\t1\t0.0\t0\t1"
## [90] "10\t1\t0.0\t1\t1"
## [91] "11\t1\t0.0\t1\t1"
## [92] "12\t2\t0.0\t1\t2"
## [93] "14\t7\t0.0\t1\t6 1"
## [94] "15\t1\t0.0\t1\t1"
## [95] "17\t5\t0.0\t1\t4 1"
## [96] "19\t1\t0.0\t1\t1"
## [97] "22\t3\t0.0\t2\t3"
## [98] "23\t2\t0.0\t2\t2"
## [99] "26\t1\t0.0\t2\t1"
## [100] "27\t1\t0.0\t2\t1"
## [101] "29\t2\t0.0\t2\t2"
## [102] "30\t1\t0.0\t3\t1"
## [103] "31\t1\t0.0\t3\t1"
## [104] "32\t2\t0.0\t3\t2"
## [105] "33\t4\t0.0\t3\t3 1"
## [106] "34\t1\t0.0\t3\t0 1"
## [107] "37\t1\t0.0\t3\t0 1"
## [108] "38\t1\t0.0\t3\t1"
## [109] "40\t2\t0.0\t4\t2"
## [110] "41\t1\t0.0\t4\t0 1"
## [111] "42\t5\t0.0\t4\t5"
## [112] "43\t1\t0.0\t4\t1"
## [113] "45\t1\t0.0\t4\t1"
## [114] "47\t2\t0.0\t4\t0 2"
## [115] "50\t1\t0.0\t4\t1"
## [116] "51\t2\t0.0\t4\t2"
## [117] "52\t2\t0.0\t4\t2"
## [118] "53\t1\t0.0\t4\t1"
## [119] "54\t1\t0.0\t4\t1"
## [120] "55\t2\t0.0\t4\t1 1"
## [121] "56\t1\t0.0\t4\t0 1"
## [122] "57\t3\t0.0\t4\t3"
## [123] "58\t2\t0.0\t4\t2"
## [124] "59\t1\t0.0\t4\t1"
## [125] "63\t2\t0.0\t4\t2"
## [126] "64\t2\t0.0\t4\t2"
## [127] "65\t1\t0.0\t4\t1"
## [128] "66\t2\t0.0\t4\t1 1"
## [129] "67\t3\t0.0\t4\t3"
## [130] "68\t2\t0.0\t4\t2"
## [131] "69\t2\t0.0\t4\t2"
## [132] "70\t1\t0.0\t4\t1"
## [133] "71\t5\t0.0\t4\t4 0 1"
## [134] "73\t3\t0.0\t4\t3"
## [135] "74\t3\t0.0\t4\t3"
## [136] "76\t1\t0.0\t4\t1"
## [137] "77\t3\t0.0\t4\t3"
## [138] "78\t1\t0.0\t4\t1"
## [139] "79\t4\t0.0\t4\t4"
## [140] "81\t1\t0.0\t4\t0 1"
## [141] "83\t1\t0.0\t4\t1"
## [142] "84\t1\t0.0\t4\t1"
## [143] "85\t3\t0.0\t4\t3"
## [144] "86\t3\t0.0\t4\t3"
## [145] "87\t2\t0.0\t4\t2"
## [146] "88\t1\t0.0\t4\t1"
## [147] "89\t2\t0.0\t4\t2"
## [148] "92\t2\t0.0\t4\t2"
## [149] "93\t1\t0.0\t4\t1"
## [150] "94\t1\t0.0\t4\t0 1"
## [151] "95\t1\t0.0\t4\t1"
## [152] "96\t1\t0.0\t4\t1"
## [153] "102\t1\t0.0\t4\t1"
## [154] "104\t1\t0.0\t4\t1"
## [155] "107\t1\t0.0\t4\t1"
## [156] "109\t1\t0.0\t4\t1"
## [157] "111\t3\t0.0\t4\t3"
## [158] "113\t1\t0.0\t4\t1"
## [159] "114\t1\t0.0\t4\t1"
## [160] "117\t1\t0.0\t4\t1"
## [161] "122\t1\t0.0\t4\t0 1"
## [162] "124\t1\t0.0\t4\t1"
## [163] "129\t1\t0.0\t4\t1"
## [164] "132\t1\t0.0\t4\t0 1"
## [165] "134\t1\t0.0\t4\t1"
## [166] "137\t1\t0.0\t4\t1"
## [167] "138\t1\t0.0\t4\t1"
## [168] "144\t1\t0.0\t4\t1"
## [169] "145\t1\t0.0\t4\t1"
## [170] "150\t1\t0.0\t4\t1"
## [171] "152\t1\t0.0\t4\t1"
## [172] "160\t1\t0.0\t4\t1"
## [173] "162\t1\t0.0\t4\t1"
## [174] "163\t1\t0.0\t4\t1"
## [175] ""
## [176] ""
## [177] "WARNING:"
## [178] " One or more of your adapter sequences may be incomplete."
## [179] " Please see the detailed output above."
##
## [[44]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/42_S44_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/42_S44_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/42_S44_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/42_S44_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.32 s (112 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 11,867"
## [9] " Read 1 with adapter: 6 (0.1%)"
## [10] " Read 2 with adapter: 176 (1.5%)"
## [11] "Pairs written (passing filters): 11,867 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 4,984,140 bp"
## [14] " Read 1: 2,325,932 bp"
## [15] " Read 2: 2,658,208 bp"
## [16] "Total written (filtered): 4,973,138 bp (99.8%)"
## [17] " Read 1: 2,325,692 bp"
## [18] " Read 2: 2,647,446 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t11.6\t0\t1"
## [30] "6\t2\t2.9\t0\t2"
## [31] ""
## [32] ""
## [33] "=== First read: Adapter 2 ==="
## [34] ""
## [35] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 3 times"
## [36] ""
## [37] "No. of allowed errors:"
## [38] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [39] ""
## [40] "Bases preceding removed adapters:"
## [41] " A: 0.0%"
## [42] " C: 0.0%"
## [43] " G: 100.0%"
## [44] " T: 0.0%"
## [45] " none/other: 0.0%"
## [46] ""
## [47] "Overview of removed sequences"
## [48] "length\tcount\texpect\tmax.err\terror counts"
## [49] "43\t1\t0.0\t2\t1"
## [50] "90\t2\t0.0\t2\t2"
## [51] ""
## [52] ""
## [53] "=== Second read: Adapter 3 ==="
## [54] ""
## [55] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [56] ""
## [57] "=== Second read: Adapter 4 ==="
## [58] ""
## [59] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 176 times"
## [60] ""
## [61] "No. of allowed errors:"
## [62] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [63] ""
## [64] "Bases preceding removed adapters:"
## [65] " A: 82.4%"
## [66] " C: 13.1%"
## [67] " G: 1.7%"
## [68] " T: 2.8%"
## [69] " none/other: 0.0%"
## [70] "WARNING:"
## [71] " The adapter is preceded by \"A\" extremely often."
## [72] " The provided adapter sequence could be incomplete at its 3' end."
## [73] ""
## [74] "Overview of removed sequences"
## [75] "length\tcount\texpect\tmax.err\terror counts"
## [76] "5\t2\t11.6\t0\t2"
## [77] "6\t3\t2.9\t0\t3"
## [78] "7\t1\t0.7\t0\t1"
## [79] "8\t3\t0.2\t0\t3"
## [80] "9\t1\t0.0\t0\t1"
## [81] "10\t1\t0.0\t1\t1"
## [82] "11\t1\t0.0\t1\t1"
## [83] "12\t3\t0.0\t1\t2 1"
## [84] "14\t8\t0.0\t1\t8"
## [85] "16\t8\t0.0\t1\t8"
## [86] "17\t3\t0.0\t1\t3"
## [87] "19\t1\t0.0\t1\t0 1"
## [88] "20\t1\t0.0\t2\t0 1"
## [89] "22\t3\t0.0\t2\t3"
## [90] "23\t1\t0.0\t2\t0 1"
## [91] "24\t1\t0.0\t2\t1"
## [92] "25\t1\t0.0\t2\t0 0 1"
## [93] "27\t2\t0.0\t2\t2"
## [94] "28\t2\t0.0\t2\t2"
## [95] "29\t1\t0.0\t2\t0 1"
## [96] "30\t1\t0.0\t3\t1"
## [97] "32\t2\t0.0\t3\t2"
## [98] "33\t3\t0.0\t3\t3"
## [99] "34\t1\t0.0\t3\t1"
## [100] "35\t2\t0.0\t3\t2"
## [101] "36\t3\t0.0\t3\t3"
## [102] "37\t1\t0.0\t3\t1"
## [103] "38\t1\t0.0\t3\t1"
## [104] "39\t1\t0.0\t3\t1"
## [105] "40\t1\t0.0\t4\t0 1"
## [106] "41\t2\t0.0\t4\t2"
## [107] "42\t3\t0.0\t4\t3"
## [108] "43\t6\t0.0\t4\t3 2 1"
## [109] "45\t1\t0.0\t4\t0 0 0 1"
## [110] "46\t2\t0.0\t4\t2"
## [111] "47\t3\t0.0\t4\t2 1"
## [112] "48\t1\t0.0\t4\t1"
## [113] "51\t2\t0.0\t4\t2"
## [114] "52\t3\t0.0\t4\t3"
## [115] "54\t2\t0.0\t4\t2"
## [116] "55\t1\t0.0\t4\t1"
## [117] "57\t1\t0.0\t4\t0 1"
## [118] "58\t2\t0.0\t4\t2"
## [119] "59\t2\t0.0\t4\t1 1"
## [120] "60\t3\t0.0\t4\t2 1"
## [121] "63\t5\t0.0\t4\t4 1"
## [122] "64\t4\t0.0\t4\t4"
## [123] "66\t1\t0.0\t4\t1"
## [124] "71\t1\t0.0\t4\t1"
## [125] "72\t3\t0.0\t4\t2 1"
## [126] "73\t1\t0.0\t4\t1"
## [127] "74\t2\t0.0\t4\t1 1"
## [128] "75\t2\t0.0\t4\t2"
## [129] "81\t1\t0.0\t4\t1"
## [130] "82\t1\t0.0\t4\t1"
## [131] "83\t1\t0.0\t4\t1"
## [132] "84\t2\t0.0\t4\t2"
## [133] "85\t2\t0.0\t4\t2"
## [134] "86\t7\t0.0\t4\t7"
## [135] "93\t1\t0.0\t4\t0 1"
## [136] "94\t2\t0.0\t4\t0 2"
## [137] "96\t2\t0.0\t4\t2"
## [138] "97\t2\t0.0\t4\t2"
## [139] "98\t3\t0.0\t4\t3"
## [140] "99\t1\t0.0\t4\t1"
## [141] "103\t2\t0.0\t4\t1 1"
## [142] "104\t2\t0.0\t4\t2"
## [143] "105\t1\t0.0\t4\t1"
## [144] "106\t1\t0.0\t4\t1"
## [145] "109\t3\t0.0\t4\t3"
## [146] "110\t3\t0.0\t4\t3"
## [147] "111\t1\t0.0\t4\t1"
## [148] "112\t1\t0.0\t4\t1"
## [149] "113\t1\t0.0\t4\t1"
## [150] "114\t1\t0.0\t4\t1"
## [151] "115\t1\t0.0\t4\t1"
## [152] "116\t1\t0.0\t4\t1"
## [153] "118\t2\t0.0\t4\t2"
## [154] "119\t1\t0.0\t4\t1"
## [155] "120\t1\t0.0\t4\t1"
## [156] "121\t2\t0.0\t4\t2"
## [157] "126\t1\t0.0\t4\t1"
## [158] "131\t1\t0.0\t4\t1"
## [159] "133\t1\t0.0\t4\t1"
## [160] "134\t1\t0.0\t4\t1"
## [161] "136\t1\t0.0\t4\t1"
## [162] "138\t1\t0.0\t4\t1"
## [163] "140\t1\t0.0\t4\t1"
## [164] "141\t1\t0.0\t4\t1"
## [165] "157\t1\t0.0\t4\t1"
## [166] "158\t1\t0.0\t4\t1"
## [167] "172\t1\t0.0\t4\t1"
## [168] ""
## [169] ""
## [170] "WARNING:"
## [171] " One or more of your adapter sequences may be incomplete."
## [172] " Please see the detailed output above."
##
## [[45]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/551_S45_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/551_S45_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/551_S45_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/551_S45_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.30 s (114 us/read; 0.53 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 11,417"
## [9] " Read 1 with adapter: 4 (0.0%)"
## [10] " Read 2 with adapter: 105 (0.9%)"
## [11] "Pairs written (passing filters): 11,417 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 4,795,140 bp"
## [14] " Read 1: 2,237,732 bp"
## [15] " Read 2: 2,557,408 bp"
## [16] "Total written (filtered): 4,788,933 bp (99.9%)"
## [17] " Read 1: 2,237,680 bp"
## [18] " Read 2: 2,551,253 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 4 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "6\t1\t2.8\t0\t1"
## [30] "12\t1\t0.0\t1\t1"
## [31] "17\t2\t0.0\t1\t1 1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 0 times"
## [37] ""
## [38] "=== Second read: Adapter 3 ==="
## [39] ""
## [40] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [41] ""
## [42] "=== Second read: Adapter 4 ==="
## [43] ""
## [44] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 105 times"
## [45] ""
## [46] "No. of allowed errors:"
## [47] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [48] ""
## [49] "Bases preceding removed adapters:"
## [50] " A: 67.6%"
## [51] " C: 25.7%"
## [52] " G: 3.8%"
## [53] " T: 2.9%"
## [54] " none/other: 0.0%"
## [55] ""
## [56] "Overview of removed sequences"
## [57] "length\tcount\texpect\tmax.err\terror counts"
## [58] "5\t7\t11.1\t0\t7"
## [59] "6\t1\t2.8\t0\t1"
## [60] "7\t1\t0.7\t0\t1"
## [61] "8\t1\t0.2\t0\t1"
## [62] "12\t2\t0.0\t1\t2"
## [63] "14\t2\t0.0\t1\t2"
## [64] "15\t1\t0.0\t1\t1"
## [65] "16\t8\t0.0\t1\t7 1"
## [66] "17\t1\t0.0\t1\t1"
## [67] "18\t1\t0.0\t1\t0 1"
## [68] "19\t1\t0.0\t1\t1"
## [69] "20\t1\t0.0\t2\t1"
## [70] "22\t1\t0.0\t2\t1"
## [71] "25\t1\t0.0\t2\t1"
## [72] "26\t2\t0.0\t2\t1 1"
## [73] "27\t1\t0.0\t2\t1"
## [74] "28\t1\t0.0\t2\t0 1"
## [75] "29\t1\t0.0\t2\t1"
## [76] "31\t3\t0.0\t3\t2 1"
## [77] "34\t1\t0.0\t3\t1"
## [78] "35\t2\t0.0\t3\t2"
## [79] "39\t2\t0.0\t3\t1 1"
## [80] "41\t2\t0.0\t4\t1 1"
## [81] "42\t1\t0.0\t4\t1"
## [82] "44\t1\t0.0\t4\t1"
## [83] "47\t2\t0.0\t4\t1 1"
## [84] "48\t2\t0.0\t4\t2"
## [85] "50\t2\t0.0\t4\t1 1"
## [86] "53\t1\t0.0\t4\t1"
## [87] "54\t1\t0.0\t4\t0 1"
## [88] "57\t1\t0.0\t4\t1"
## [89] "58\t1\t0.0\t4\t1"
## [90] "59\t2\t0.0\t4\t2"
## [91] "62\t1\t0.0\t4\t0 1"
## [92] "63\t2\t0.0\t4\t2"
## [93] "65\t2\t0.0\t4\t2"
## [94] "67\t1\t0.0\t4\t1"
## [95] "72\t3\t0.0\t4\t3"
## [96] "73\t1\t0.0\t4\t1"
## [97] "76\t1\t0.0\t4\t1"
## [98] "79\t2\t0.0\t4\t2"
## [99] "82\t1\t0.0\t4\t1"
## [100] "84\t3\t0.0\t4\t3"
## [101] "86\t2\t0.0\t4\t0 2"
## [102] "87\t1\t0.0\t4\t1"
## [103] "88\t2\t0.0\t4\t2"
## [104] "89\t1\t0.0\t4\t0 1"
## [105] "96\t1\t0.0\t4\t1"
## [106] "98\t3\t0.0\t4\t3"
## [107] "102\t1\t0.0\t4\t1"
## [108] "103\t1\t0.0\t4\t1"
## [109] "104\t2\t0.0\t4\t2"
## [110] "105\t3\t0.0\t4\t3"
## [111] "113\t2\t0.0\t4\t2"
## [112] "115\t1\t0.0\t4\t1"
## [113] "118\t1\t0.0\t4\t1"
## [114] "119\t1\t0.0\t4\t1"
## [115] "121\t1\t0.0\t4\t1"
## [116] "127\t1\t0.0\t4\t1"
## [117] "133\t1\t0.0\t4\t1"
## [118] "140\t1\t0.0\t4\t1"
## [119] "143\t1\t0.0\t4\t1"
## [120] "146\t1\t0.0\t4\t1"
## [121] "149\t1\t0.0\t4\t0 1"
## [122] "153\t1\t0.0\t4\t1"
##
## [[46]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/552_S46_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/552_S46_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/552_S46_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/552_S46_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.59 s (116 us/read; 0.52 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 13,753"
## [9] " Read 1 with adapter: 6 (0.0%)"
## [10] " Read 2 with adapter: 185 (1.3%)"
## [11] "Pairs written (passing filters): 13,753 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 5,776,260 bp"
## [14] " Read 1: 2,695,588 bp"
## [15] " Read 2: 3,080,672 bp"
## [16] "Total written (filtered): 5,764,090 bp (99.8%)"
## [17] " Read 1: 2,695,421 bp"
## [18] " Read 2: 3,068,669 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t13.4\t0\t1"
## [30] "11\t1\t0.0\t1\t1"
## [31] "29\t1\t0.0\t2\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 3 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 66.7%"
## [43] " C: 33.3%"
## [44] " G: 0.0%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "16\t1\t0.0\t1\t1"
## [51] "42\t1\t0.0\t2\t1"
## [52] "64\t1\t0.0\t2\t1"
## [53] ""
## [54] ""
## [55] "=== Second read: Adapter 3 ==="
## [56] ""
## [57] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 4 times"
## [58] ""
## [59] "No. of allowed errors:"
## [60] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [61] ""
## [62] "Overview of removed sequences"
## [63] "length\tcount\texpect\tmax.err\terror counts"
## [64] "5\t2\t13.4\t0\t2"
## [65] "12\t1\t0.0\t1\t1"
## [66] "25\t1\t0.0\t2\t1"
## [67] ""
## [68] ""
## [69] "=== Second read: Adapter 4 ==="
## [70] ""
## [71] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 183 times"
## [72] ""
## [73] "No. of allowed errors:"
## [74] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [75] ""
## [76] "Bases preceding removed adapters:"
## [77] " A: 63.9%"
## [78] " C: 33.3%"
## [79] " G: 0.5%"
## [80] " T: 2.2%"
## [81] " none/other: 0.0%"
## [82] ""
## [83] "Overview of removed sequences"
## [84] "length\tcount\texpect\tmax.err\terror counts"
## [85] "5\t7\t13.4\t0\t7"
## [86] "6\t3\t3.4\t0\t3"
## [87] "7\t2\t0.8\t0\t2"
## [88] "8\t4\t0.2\t0\t4"
## [89] "10\t2\t0.0\t1\t1 1"
## [90] "12\t2\t0.0\t1\t2"
## [91] "13\t2\t0.0\t1\t2"
## [92] "14\t1\t0.0\t1\t1"
## [93] "16\t2\t0.0\t1\t2"
## [94] "17\t1\t0.0\t1\t1"
## [95] "18\t1\t0.0\t1\t1"
## [96] "19\t3\t0.0\t1\t3"
## [97] "20\t1\t0.0\t2\t1"
## [98] "22\t7\t0.0\t2\t7"
## [99] "23\t1\t0.0\t2\t1"
## [100] "24\t1\t0.0\t2\t1"
## [101] "25\t1\t0.0\t2\t1"
## [102] "28\t2\t0.0\t2\t2"
## [103] "31\t3\t0.0\t3\t3"
## [104] "32\t2\t0.0\t3\t1 1"
## [105] "33\t3\t0.0\t3\t3"
## [106] "34\t1\t0.0\t3\t1"
## [107] "35\t1\t0.0\t3\t0 1"
## [108] "36\t1\t0.0\t3\t1"
## [109] "37\t1\t0.0\t3\t1"
## [110] "38\t1\t0.0\t3\t1"
## [111] "40\t3\t0.0\t4\t3"
## [112] "41\t1\t0.0\t4\t1"
## [113] "42\t3\t0.0\t4\t2 1"
## [114] "44\t2\t0.0\t4\t1 0 1"
## [115] "45\t2\t0.0\t4\t2"
## [116] "46\t2\t0.0\t4\t2"
## [117] "47\t3\t0.0\t4\t2 1"
## [118] "48\t1\t0.0\t4\t0 1"
## [119] "49\t1\t0.0\t4\t0 0 1"
## [120] "50\t2\t0.0\t4\t2"
## [121] "51\t2\t0.0\t4\t2"
## [122] "52\t3\t0.0\t4\t2 1"
## [123] "54\t1\t0.0\t4\t1"
## [124] "57\t1\t0.0\t4\t0 1"
## [125] "58\t3\t0.0\t4\t3"
## [126] "59\t2\t0.0\t4\t0 2"
## [127] "60\t1\t0.0\t4\t1"
## [128] "62\t1\t0.0\t4\t1"
## [129] "64\t1\t0.0\t4\t0 1"
## [130] "65\t3\t0.0\t4\t2 1"
## [131] "66\t1\t0.0\t4\t1"
## [132] "69\t1\t0.0\t4\t1"
## [133] "70\t1\t0.0\t4\t0 1"
## [134] "71\t1\t0.0\t4\t1"
## [135] "72\t2\t0.0\t4\t2"
## [136] "73\t2\t0.0\t4\t2"
## [137] "74\t3\t0.0\t4\t3"
## [138] "77\t1\t0.0\t4\t1"
## [139] "78\t1\t0.0\t4\t1"
## [140] "79\t7\t0.0\t4\t7"
## [141] "80\t2\t0.0\t4\t2"
## [142] "82\t2\t0.0\t4\t2"
## [143] "83\t2\t0.0\t4\t1 1"
## [144] "84\t1\t0.0\t4\t0 0 1"
## [145] "85\t2\t0.0\t4\t2"
## [146] "86\t1\t0.0\t4\t1"
## [147] "87\t1\t0.0\t4\t1"
## [148] "88\t3\t0.0\t4\t3"
## [149] "89\t1\t0.0\t4\t1"
## [150] "90\t1\t0.0\t4\t1"
## [151] "92\t4\t0.0\t4\t4"
## [152] "93\t2\t0.0\t4\t2"
## [153] "94\t1\t0.0\t4\t1"
## [154] "95\t3\t0.0\t4\t2 1"
## [155] "99\t1\t0.0\t4\t1"
## [156] "100\t1\t0.0\t4\t1"
## [157] "101\t2\t0.0\t4\t2"
## [158] "102\t1\t0.0\t4\t1"
## [159] "103\t1\t0.0\t4\t1"
## [160] "104\t2\t0.0\t4\t2"
## [161] "105\t6\t0.0\t4\t6"
## [162] "106\t1\t0.0\t4\t1"
## [163] "108\t2\t0.0\t4\t2"
## [164] "111\t2\t0.0\t4\t2"
## [165] "112\t1\t0.0\t4\t1"
## [166] "113\t1\t0.0\t4\t1"
## [167] "114\t1\t0.0\t4\t1"
## [168] "115\t1\t0.0\t4\t1"
## [169] "118\t1\t0.0\t4\t1"
## [170] "120\t1\t0.0\t4\t1"
## [171] "121\t2\t0.0\t4\t1 1"
## [172] "122\t1\t0.0\t4\t1"
## [173] "123\t1\t0.0\t4\t1"
## [174] "124\t1\t0.0\t4\t1"
## [175] "126\t1\t0.0\t4\t1"
## [176] "127\t1\t0.0\t4\t0 1"
## [177] "136\t1\t0.0\t4\t1"
## [178] "138\t2\t0.0\t4\t2"
## [179] "143\t1\t0.0\t4\t1"
## [180] "145\t1\t0.0\t4\t1"
## [181] "148\t1\t0.0\t4\t1"
## [182] "150\t1\t0.0\t4\t1"
## [183] "154\t1\t0.0\t4\t1"
## [184] "156\t1\t0.0\t4\t1"
## [185] "159\t1\t0.0\t4\t1"
## [186] "174\t1\t0.0\t4\t1"
##
## [[47]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/553_S47_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/553_S47_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/553_S47_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/553_S47_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.41 s (115 us/read; 0.52 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 12,254"
## [9] " Read 1 with adapter: 5 (0.0%)"
## [10] " Read 2 with adapter: 139 (1.1%)"
## [11] "Pairs written (passing filters): 12,253 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 5,146,680 bp"
## [14] " Read 1: 2,401,784 bp"
## [15] " Read 2: 2,744,896 bp"
## [16] "Total written (filtered): 5,138,010 bp (99.8%)"
## [17] " Read 1: 2,401,375 bp"
## [18] " Read 2: 2,736,635 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 4 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "9\t1\t0.0\t0\t1"
## [30] "14\t1\t0.0\t1\t0 1"
## [31] "21\t1\t0.0\t2\t1"
## [32] "25\t1\t0.0\t2\t1"
## [33] ""
## [34] ""
## [35] "=== First read: Adapter 2 ==="
## [36] ""
## [37] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 1 times"
## [38] ""
## [39] "No. of allowed errors:"
## [40] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [41] ""
## [42] "Bases preceding removed adapters:"
## [43] " A: 100.0%"
## [44] " C: 0.0%"
## [45] " G: 0.0%"
## [46] " T: 0.0%"
## [47] " none/other: 0.0%"
## [48] ""
## [49] "Overview of removed sequences"
## [50] "length\tcount\texpect\tmax.err\terror counts"
## [51] "144\t1\t0.0\t2\t1"
## [52] ""
## [53] ""
## [54] "=== Second read: Adapter 3 ==="
## [55] ""
## [56] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [57] ""
## [58] "No. of allowed errors:"
## [59] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [60] ""
## [61] "Overview of removed sequences"
## [62] "length\tcount\texpect\tmax.err\terror counts"
## [63] "18\t1\t0.0\t1\t1"
## [64] ""
## [65] ""
## [66] "=== Second read: Adapter 4 ==="
## [67] ""
## [68] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 138 times"
## [69] ""
## [70] "No. of allowed errors:"
## [71] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [72] ""
## [73] "Bases preceding removed adapters:"
## [74] " A: 79.7%"
## [75] " C: 17.4%"
## [76] " G: 2.9%"
## [77] " T: 0.0%"
## [78] " none/other: 0.0%"
## [79] ""
## [80] "Overview of removed sequences"
## [81] "length\tcount\texpect\tmax.err\terror counts"
## [82] "5\t7\t12.0\t0\t7"
## [83] "6\t1\t3.0\t0\t1"
## [84] "7\t1\t0.7\t0\t1"
## [85] "8\t4\t0.2\t0\t4"
## [86] "12\t4\t0.0\t1\t4"
## [87] "14\t6\t0.0\t1\t5 1"
## [88] "15\t1\t0.0\t1\t1"
## [89] "16\t1\t0.0\t1\t1"
## [90] "17\t3\t0.0\t1\t2 1"
## [91] "19\t1\t0.0\t1\t1"
## [92] "20\t1\t0.0\t2\t1"
## [93] "21\t3\t0.0\t2\t2 0 1"
## [94] "23\t1\t0.0\t2\t1"
## [95] "24\t3\t0.0\t2\t2 1"
## [96] "25\t1\t0.0\t2\t1"
## [97] "26\t1\t0.0\t2\t1"
## [98] "30\t1\t0.0\t3\t1"
## [99] "31\t2\t0.0\t3\t2"
## [100] "32\t2\t0.0\t3\t2"
## [101] "33\t1\t0.0\t3\t1"
## [102] "34\t1\t0.0\t3\t1"
## [103] "35\t4\t0.0\t3\t3 1"
## [104] "37\t1\t0.0\t3\t0 1"
## [105] "38\t2\t0.0\t3\t2"
## [106] "39\t2\t0.0\t3\t2"
## [107] "40\t1\t0.0\t4\t1"
## [108] "41\t4\t0.0\t4\t4"
## [109] "42\t1\t0.0\t4\t1"
## [110] "43\t4\t0.0\t4\t3 1"
## [111] "44\t1\t0.0\t4\t1"
## [112] "47\t1\t0.0\t4\t0 1"
## [113] "48\t1\t0.0\t4\t1"
## [114] "51\t1\t0.0\t4\t0 1"
## [115] "52\t1\t0.0\t4\t1"
## [116] "53\t1\t0.0\t4\t1"
## [117] "55\t2\t0.0\t4\t1 1"
## [118] "59\t3\t0.0\t4\t3"
## [119] "60\t1\t0.0\t4\t0 1"
## [120] "61\t1\t0.0\t4\t1"
## [121] "62\t3\t0.0\t4\t3"
## [122] "63\t2\t0.0\t4\t1 0 1"
## [123] "64\t3\t0.0\t4\t3"
## [124] "65\t1\t0.0\t4\t1"
## [125] "70\t1\t0.0\t4\t1"
## [126] "71\t1\t0.0\t4\t1"
## [127] "74\t3\t0.0\t4\t3"
## [128] "79\t1\t0.0\t4\t1"
## [129] "80\t1\t0.0\t4\t1"
## [130] "84\t2\t0.0\t4\t1 0 1"
## [131] "85\t2\t0.0\t4\t2"
## [132] "87\t1\t0.0\t4\t0 1"
## [133] "89\t1\t0.0\t4\t1"
## [134] "92\t1\t0.0\t4\t1"
## [135] "93\t1\t0.0\t4\t1"
## [136] "94\t2\t0.0\t4\t2"
## [137] "98\t1\t0.0\t4\t1"
## [138] "100\t3\t0.0\t4\t3"
## [139] "101\t1\t0.0\t4\t1"
## [140] "102\t1\t0.0\t4\t1"
## [141] "103\t1\t0.0\t4\t1"
## [142] "104\t1\t0.0\t4\t1"
## [143] "105\t7\t0.0\t4\t7"
## [144] "106\t2\t0.0\t4\t2"
## [145] "107\t1\t0.0\t4\t1"
## [146] "109\t1\t0.0\t4\t1"
## [147] "110\t1\t0.0\t4\t1"
## [148] "111\t1\t0.0\t4\t1"
## [149] "116\t1\t0.0\t4\t1"
## [150] "120\t1\t0.0\t4\t1"
## [151] "121\t1\t0.0\t4\t1"
## [152] "125\t1\t0.0\t4\t1"
## [153] "126\t1\t0.0\t4\t1"
## [154] "127\t1\t0.0\t4\t0 1"
## [155] "132\t2\t0.0\t4\t2"
## [156] "150\t1\t0.0\t4\t1"
## [157] "151\t1\t0.0\t4\t1"
## [158] "160\t1\t0.0\t4\t1"
## [159] "172\t1\t0.0\t4\t1"
## [160] "179\t1\t0.0\t4\t1"
##
## [[48]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/554_S48_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/554_S48_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/554_S48_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/554_S48_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.46 s (113 us/read; 0.53 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 12,965"
## [9] " Read 1 with adapter: 4 (0.0%)"
## [10] " Read 2 with adapter: 122 (0.9%)"
## [11] "Pairs written (passing filters): 12,964 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 5,445,300 bp"
## [14] " Read 1: 2,541,140 bp"
## [15] " Read 2: 2,904,160 bp"
## [16] "Total written (filtered): 5,437,236 bp (99.9%)"
## [17] " Read 1: 2,540,750 bp"
## [18] " Read 2: 2,896,486 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "8\t1\t0.2\t0\t1"
## [30] "18\t1\t0.0\t1\t1"
## [31] "28\t1\t0.0\t2\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 1 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 100.0%"
## [43] " C: 0.0%"
## [44] " G: 0.0%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "140\t1\t0.0\t2\t1"
## [51] ""
## [52] ""
## [53] "=== Second read: Adapter 3 ==="
## [54] ""
## [55] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 2 times"
## [56] ""
## [57] "No. of allowed errors:"
## [58] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [59] ""
## [60] "Overview of removed sequences"
## [61] "length\tcount\texpect\tmax.err\terror counts"
## [62] "5\t2\t12.7\t0\t2"
## [63] ""
## [64] ""
## [65] "=== Second read: Adapter 4 ==="
## [66] ""
## [67] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 122 times"
## [68] ""
## [69] "No. of allowed errors:"
## [70] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [71] ""
## [72] "Bases preceding removed adapters:"
## [73] " A: 91.0%"
## [74] " C: 5.7%"
## [75] " G: 2.5%"
## [76] " T: 0.8%"
## [77] " none/other: 0.0%"
## [78] "WARNING:"
## [79] " The adapter is preceded by \"A\" extremely often."
## [80] " The provided adapter sequence could be incomplete at its 3' end."
## [81] ""
## [82] "Overview of removed sequences"
## [83] "length\tcount\texpect\tmax.err\terror counts"
## [84] "5\t2\t12.7\t0\t2"
## [85] "6\t1\t3.2\t0\t1"
## [86] "7\t1\t0.8\t0\t1"
## [87] "8\t2\t0.2\t0\t2"
## [88] "10\t1\t0.0\t1\t1"
## [89] "11\t2\t0.0\t1\t2"
## [90] "14\t2\t0.0\t1\t1 1"
## [91] "16\t4\t0.0\t1\t4"
## [92] "17\t1\t0.0\t1\t1"
## [93] "19\t1\t0.0\t1\t0 1"
## [94] "20\t2\t0.0\t2\t2"
## [95] "21\t1\t0.0\t2\t1"
## [96] "22\t1\t0.0\t2\t1"
## [97] "23\t1\t0.0\t2\t1"
## [98] "27\t1\t0.0\t2\t1"
## [99] "28\t1\t0.0\t2\t1"
## [100] "29\t2\t0.0\t2\t2"
## [101] "30\t2\t0.0\t3\t1 1"
## [102] "31\t2\t0.0\t3\t1 1"
## [103] "33\t2\t0.0\t3\t1 1"
## [104] "34\t3\t0.0\t3\t2 0 1"
## [105] "35\t3\t0.0\t3\t2 1"
## [106] "36\t2\t0.0\t3\t1 1"
## [107] "37\t2\t0.0\t3\t1 0 0 1"
## [108] "39\t1\t0.0\t3\t1"
## [109] "41\t2\t0.0\t4\t2"
## [110] "42\t2\t0.0\t4\t2"
## [111] "43\t2\t0.0\t4\t2"
## [112] "44\t1\t0.0\t4\t1"
## [113] "45\t1\t0.0\t4\t1"
## [114] "47\t2\t0.0\t4\t1 1"
## [115] "48\t1\t0.0\t4\t1"
## [116] "49\t1\t0.0\t4\t1"
## [117] "51\t3\t0.0\t4\t1 0 1 1"
## [118] "52\t1\t0.0\t4\t1"
## [119] "53\t1\t0.0\t4\t1"
## [120] "54\t1\t0.0\t4\t1"
## [121] "55\t3\t0.0\t4\t3"
## [122] "58\t2\t0.0\t4\t2"
## [123] "60\t1\t0.0\t4\t0 1"
## [124] "62\t2\t0.0\t4\t2"
## [125] "63\t1\t0.0\t4\t1"
## [126] "64\t1\t0.0\t4\t1"
## [127] "65\t1\t0.0\t4\t1"
## [128] "66\t1\t0.0\t4\t1"
## [129] "71\t1\t0.0\t4\t1"
## [130] "72\t3\t0.0\t4\t3"
## [131] "73\t1\t0.0\t4\t1"
## [132] "74\t1\t0.0\t4\t1"
## [133] "75\t1\t0.0\t4\t1"
## [134] "76\t2\t0.0\t4\t2"
## [135] "78\t1\t0.0\t4\t1"
## [136] "79\t1\t0.0\t4\t1"
## [137] "83\t1\t0.0\t4\t1"
## [138] "84\t1\t0.0\t4\t1"
## [139] "86\t1\t0.0\t4\t0 1"
## [140] "90\t2\t0.0\t4\t2"
## [141] "91\t1\t0.0\t4\t0 1"
## [142] "93\t1\t0.0\t4\t1"
## [143] "94\t2\t0.0\t4\t2"
## [144] "95\t2\t0.0\t4\t2"
## [145] "98\t3\t0.0\t4\t3"
## [146] "100\t1\t0.0\t4\t1"
## [147] "101\t3\t0.0\t4\t3"
## [148] "104\t2\t0.0\t4\t2"
## [149] "105\t1\t0.0\t4\t1"
## [150] "107\t1\t0.0\t4\t1"
## [151] "108\t1\t0.0\t4\t1"
## [152] "113\t3\t0.0\t4\t3"
## [153] "119\t1\t0.0\t4\t0 1"
## [154] "121\t1\t0.0\t4\t1"
## [155] "123\t1\t0.0\t4\t1"
## [156] "124\t1\t0.0\t4\t1"
## [157] "130\t2\t0.0\t4\t2"
## [158] "143\t1\t0.0\t4\t0 1"
## [159] "148\t1\t0.0\t4\t1"
## [160] "150\t2\t0.0\t4\t2"
## [161] "160\t1\t0.0\t4\t1"
## [162] "176\t1\t0.0\t4\t1"
## [163] ""
## [164] ""
## [165] "WARNING:"
## [166] " One or more of your adapter sequences may be incomplete."
## [167] " Please see the detailed output above."
##
## [[49]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/55RNA1_S49_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/55RNA1_S49_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/55RNA1_S49_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/55RNA1_S49_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.91 s (116 us/read; 0.52 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 7,835"
## [9] " Read 1 with adapter: 38 (0.5%)"
## [10] " Read 2 with adapter: 234 (3.0%)"
## [11] "Pairs written (passing filters): 7,834 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,290,700 bp"
## [14] " Read 1: 1,535,660 bp"
## [15] " Read 2: 1,755,040 bp"
## [16] "Total written (filtered): 3,271,489 bp (99.4%)"
## [17] " Read 1: 1,533,204 bp"
## [18] " Read 2: 1,738,285 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 2 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t7.7\t0\t1"
## [30] "14\t1\t0.0\t1\t0 1"
## [31] ""
## [32] ""
## [33] "=== First read: Adapter 2 ==="
## [34] ""
## [35] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 36 times"
## [36] ""
## [37] "No. of allowed errors:"
## [38] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [39] ""
## [40] "Bases preceding removed adapters:"
## [41] " A: 16.7%"
## [42] " C: 11.1%"
## [43] " G: 72.2%"
## [44] " T: 0.0%"
## [45] " none/other: 0.0%"
## [46] ""
## [47] "Overview of removed sequences"
## [48] "length\tcount\texpect\tmax.err\terror counts"
## [49] "5\t1\t7.7\t0\t1"
## [50] "6\t1\t1.9\t0\t1"
## [51] "9\t2\t0.0\t0\t2"
## [52] "12\t1\t0.0\t1\t1"
## [53] "16\t3\t0.0\t1\t3"
## [54] "23\t1\t0.0\t2\t1"
## [55] "27\t1\t0.0\t2\t1"
## [56] "35\t1\t0.0\t2\t1"
## [57] "36\t3\t0.0\t2\t3"
## [58] "64\t1\t0.0\t2\t1"
## [59] "81\t2\t0.0\t2\t2"
## [60] "82\t1\t0.0\t2\t1"
## [61] "83\t1\t0.0\t2\t1"
## [62] "90\t15\t0.0\t2\t15"
## [63] "109\t2\t0.0\t2\t2"
## [64] ""
## [65] ""
## [66] "=== Second read: Adapter 3 ==="
## [67] ""
## [68] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [69] ""
## [70] "=== Second read: Adapter 4 ==="
## [71] ""
## [72] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 234 times"
## [73] ""
## [74] "No. of allowed errors:"
## [75] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [76] ""
## [77] "Bases preceding removed adapters:"
## [78] " A: 82.1%"
## [79] " C: 12.8%"
## [80] " G: 2.1%"
## [81] " T: 3.0%"
## [82] " none/other: 0.0%"
## [83] "WARNING:"
## [84] " The adapter is preceded by \"A\" extremely often."
## [85] " The provided adapter sequence could be incomplete at its 3' end."
## [86] ""
## [87] "Overview of removed sequences"
## [88] "length\tcount\texpect\tmax.err\terror counts"
## [89] "5\t2\t7.7\t0\t2"
## [90] "6\t5\t1.9\t0\t5"
## [91] "7\t3\t0.5\t0\t3"
## [92] "8\t6\t0.1\t0\t6"
## [93] "11\t2\t0.0\t1\t2"
## [94] "12\t3\t0.0\t1\t2 1"
## [95] "13\t3\t0.0\t1\t3"
## [96] "14\t6\t0.0\t1\t6"
## [97] "15\t3\t0.0\t1\t3"
## [98] "16\t1\t0.0\t1\t1"
## [99] "17\t1\t0.0\t1\t1"
## [100] "19\t2\t0.0\t1\t2"
## [101] "21\t1\t0.0\t2\t1"
## [102] "22\t2\t0.0\t2\t2"
## [103] "23\t3\t0.0\t2\t2 0 1"
## [104] "24\t1\t0.0\t2\t1"
## [105] "25\t3\t0.0\t2\t0 2 1"
## [106] "26\t1\t0.0\t2\t1"
## [107] "27\t6\t0.0\t2\t5 0 1"
## [108] "28\t2\t0.0\t2\t1 1"
## [109] "29\t1\t0.0\t2\t1"
## [110] "30\t2\t0.0\t3\t1 1"
## [111] "32\t1\t0.0\t3\t1"
## [112] "33\t4\t0.0\t3\t4"
## [113] "34\t1\t0.0\t3\t1"
## [114] "35\t3\t0.0\t3\t2 1"
## [115] "36\t1\t0.0\t3\t1"
## [116] "37\t2\t0.0\t3\t0 1 1"
## [117] "39\t1\t0.0\t3\t1"
## [118] "40\t5\t0.0\t4\t2 2 0 1"
## [119] "42\t2\t0.0\t4\t2"
## [120] "43\t2\t0.0\t4\t1 1"
## [121] "44\t6\t0.0\t4\t4 1 1"
## [122] "45\t1\t0.0\t4\t1"
## [123] "46\t3\t0.0\t4\t2 0 1"
## [124] "47\t1\t0.0\t4\t1"
## [125] "50\t3\t0.0\t4\t3"
## [126] "51\t2\t0.0\t4\t2"
## [127] "52\t1\t0.0\t4\t0 1"
## [128] "53\t2\t0.0\t4\t2"
## [129] "55\t3\t0.0\t4\t3"
## [130] "56\t1\t0.0\t4\t0 1"
## [131] "58\t1\t0.0\t4\t1"
## [132] "59\t1\t0.0\t4\t1"
## [133] "60\t1\t0.0\t4\t1"
## [134] "62\t3\t0.0\t4\t3"
## [135] "63\t3\t0.0\t4\t3"
## [136] "64\t4\t0.0\t4\t3 1"
## [137] "66\t1\t0.0\t4\t1"
## [138] "67\t1\t0.0\t4\t1"
## [139] "69\t1\t0.0\t4\t1"
## [140] "71\t1\t0.0\t4\t1"
## [141] "74\t1\t0.0\t4\t1"
## [142] "75\t2\t0.0\t4\t2"
## [143] "76\t1\t0.0\t4\t0 1"
## [144] "79\t3\t0.0\t4\t3"
## [145] "82\t1\t0.0\t4\t1"
## [146] "84\t2\t0.0\t4\t2"
## [147] "85\t6\t0.0\t4\t5 0 1"
## [148] "86\t7\t0.0\t4\t7"
## [149] "87\t2\t0.0\t4\t1 1"
## [150] "88\t2\t0.0\t4\t2"
## [151] "90\t1\t0.0\t4\t1"
## [152] "92\t1\t0.0\t4\t1"
## [153] "93\t1\t0.0\t4\t1"
## [154] "94\t2\t0.0\t4\t2"
## [155] "95\t1\t0.0\t4\t1"
## [156] "98\t2\t0.0\t4\t2"
## [157] "100\t2\t0.0\t4\t2"
## [158] "101\t1\t0.0\t4\t1"
## [159] "102\t4\t0.0\t4\t4"
## [160] "103\t3\t0.0\t4\t2 1"
## [161] "105\t3\t0.0\t4\t3"
## [162] "107\t2\t0.0\t4\t2"
## [163] "108\t2\t0.0\t4\t2"
## [164] "109\t1\t0.0\t4\t1"
## [165] "110\t2\t0.0\t4\t1 1"
## [166] "111\t2\t0.0\t4\t1 1"
## [167] "112\t1\t0.0\t4\t1"
## [168] "114\t3\t0.0\t4\t3"
## [169] "116\t3\t0.0\t4\t3"
## [170] "117\t1\t0.0\t4\t1"
## [171] "118\t15\t0.0\t4\t13 2"
## [172] "119\t1\t0.0\t4\t1"
## [173] "121\t2\t0.0\t4\t2"
## [174] "124\t1\t0.0\t4\t1"
## [175] "125\t1\t0.0\t4\t1"
## [176] "126\t2\t0.0\t4\t2"
## [177] "128\t1\t0.0\t4\t1"
## [178] "130\t1\t0.0\t4\t1"
## [179] "132\t1\t0.0\t4\t1"
## [180] "134\t1\t0.0\t4\t1"
## [181] "135\t1\t0.0\t4\t1"
## [182] "137\t2\t0.0\t4\t2"
## [183] "138\t2\t0.0\t4\t1 1"
## [184] "139\t2\t0.0\t4\t2"
## [185] "145\t1\t0.0\t4\t1"
## [186] "147\t3\t0.0\t4\t3"
## [187] "148\t1\t0.0\t4\t1"
## [188] "152\t1\t0.0\t4\t1"
## [189] "153\t1\t0.0\t4\t1"
## [190] "158\t2\t0.0\t4\t1 1"
## [191] "159\t1\t0.0\t4\t1"
## [192] "160\t2\t0.0\t4\t2"
## [193] "171\t2\t0.0\t4\t2"
## [194] "178\t1\t0.0\t4\t1"
## [195] ""
## [196] ""
## [197] "WARNING:"
## [198] " One or more of your adapter sequences may be incomplete."
## [199] " Please see the detailed output above."
##
## [[50]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/55RNA2_S50_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/55RNA2_S50_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/55RNA2_S50_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/55RNA2_S50_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.06 s (113 us/read; 0.53 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 9,385"
## [9] " Read 1 with adapter: 55 (0.6%)"
## [10] " Read 2 with adapter: 354 (3.8%)"
## [11] "Pairs written (passing filters): 9,385 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,941,700 bp"
## [14] " Read 1: 1,839,460 bp"
## [15] " Read 2: 2,102,240 bp"
## [16] "Total written (filtered): 3,911,285 bp (99.2%)"
## [17] " Read 1: 1,835,958 bp"
## [18] " Read 2: 2,075,327 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "7\t1\t0.6\t0\t1"
## [30] "8\t1\t0.1\t0\t1"
## [31] "26\t1\t0.0\t2\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 52 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 9.6%"
## [43] " C: 7.7%"
## [44] " G: 82.7%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] "WARNING:"
## [48] " The adapter is preceded by \"G\" extremely often."
## [49] " The provided adapter sequence could be incomplete at its 3' end."
## [50] ""
## [51] "Overview of removed sequences"
## [52] "length\tcount\texpect\tmax.err\terror counts"
## [53] "5\t1\t9.2\t0\t1"
## [54] "7\t1\t0.6\t0\t1"
## [55] "8\t1\t0.1\t0\t1"
## [56] "9\t1\t0.0\t0\t1"
## [57] "11\t1\t0.0\t1\t1"
## [58] "12\t1\t0.0\t1\t1"
## [59] "16\t1\t0.0\t1\t0 1"
## [60] "17\t3\t0.0\t1\t3"
## [61] "18\t1\t0.0\t1\t1"
## [62] "26\t2\t0.0\t2\t2"
## [63] "36\t5\t0.0\t2\t4 1"
## [64] "41\t1\t0.0\t2\t1"
## [65] "61\t1\t0.0\t2\t1"
## [66] "69\t1\t0.0\t2\t1"
## [67] "77\t1\t0.0\t2\t1"
## [68] "82\t5\t0.0\t2\t5"
## [69] "90\t19\t0.0\t2\t18 0 1"
## [70] "109\t3\t0.0\t2\t3"
## [71] "123\t1\t0.0\t2\t1"
## [72] "131\t1\t0.0\t2\t1"
## [73] "143\t1\t0.0\t2\t1"
## [74] ""
## [75] ""
## [76] "=== Second read: Adapter 3 ==="
## [77] ""
## [78] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [79] ""
## [80] "No. of allowed errors:"
## [81] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [82] ""
## [83] "Overview of removed sequences"
## [84] "length\tcount\texpect\tmax.err\terror counts"
## [85] "8\t1\t0.1\t0\t1"
## [86] ""
## [87] ""
## [88] "=== Second read: Adapter 4 ==="
## [89] ""
## [90] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 353 times"
## [91] ""
## [92] "No. of allowed errors:"
## [93] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [94] ""
## [95] "Bases preceding removed adapters:"
## [96] " A: 80.2%"
## [97] " C: 15.0%"
## [98] " G: 1.1%"
## [99] " T: 3.7%"
## [100] " none/other: 0.0%"
## [101] "WARNING:"
## [102] " The adapter is preceded by \"A\" extremely often."
## [103] " The provided adapter sequence could be incomplete at its 3' end."
## [104] ""
## [105] "Overview of removed sequences"
## [106] "length\tcount\texpect\tmax.err\terror counts"
## [107] "5\t2\t9.2\t0\t2"
## [108] "6\t1\t2.3\t0\t1"
## [109] "7\t1\t0.6\t0\t1"
## [110] "8\t3\t0.1\t0\t3"
## [111] "10\t1\t0.0\t1\t1"
## [112] "11\t2\t0.0\t1\t2"
## [113] "12\t3\t0.0\t1\t2 1"
## [114] "13\t1\t0.0\t1\t1"
## [115] "14\t8\t0.0\t1\t7 1"
## [116] "15\t1\t0.0\t1\t1"
## [117] "16\t8\t0.0\t1\t8"
## [118] "18\t3\t0.0\t1\t2 1"
## [119] "19\t2\t0.0\t1\t2"
## [120] "20\t2\t0.0\t2\t2"
## [121] "21\t1\t0.0\t2\t1"
## [122] "22\t4\t0.0\t2\t4"
## [123] "23\t1\t0.0\t2\t0 1"
## [124] "24\t1\t0.0\t2\t1"
## [125] "25\t3\t0.0\t2\t1 2"
## [126] "26\t1\t0.0\t2\t1"
## [127] "27\t7\t0.0\t2\t4 3"
## [128] "28\t3\t0.0\t2\t3"
## [129] "30\t2\t0.0\t3\t2"
## [130] "31\t1\t0.0\t3\t0 1"
## [131] "32\t4\t0.0\t3\t2 1 0 1"
## [132] "33\t4\t0.0\t3\t4"
## [133] "34\t1\t0.0\t3\t1"
## [134] "35\t5\t0.0\t3\t5"
## [135] "36\t5\t0.0\t3\t5"
## [136] "37\t2\t0.0\t3\t2"
## [137] "38\t2\t0.0\t3\t1 0 1"
## [138] "39\t2\t0.0\t3\t2"
## [139] "40\t3\t0.0\t4\t0 1 2"
## [140] "41\t1\t0.0\t4\t1"
## [141] "42\t3\t0.0\t4\t3"
## [142] "43\t3\t0.0\t4\t3"
## [143] "44\t2\t0.0\t4\t1 0 0 1"
## [144] "45\t6\t0.0\t4\t4 1 0 1"
## [145] "46\t2\t0.0\t4\t1 0 0 0 1"
## [146] "50\t1\t0.0\t4\t1"
## [147] "51\t2\t0.0\t4\t1 0 0 1"
## [148] "52\t4\t0.0\t4\t4"
## [149] "53\t4\t0.0\t4\t4"
## [150] "54\t5\t0.0\t4\t4 1"
## [151] "55\t4\t0.0\t4\t3 1"
## [152] "57\t3\t0.0\t4\t3"
## [153] "58\t1\t0.0\t4\t1"
## [154] "59\t5\t0.0\t4\t4 0 1"
## [155] "60\t1\t0.0\t4\t0 1"
## [156] "61\t2\t0.0\t4\t2"
## [157] "62\t4\t0.0\t4\t4"
## [158] "63\t6\t0.0\t4\t6"
## [159] "64\t10\t0.0\t4\t9 0 0 1"
## [160] "65\t10\t0.0\t4\t9 1"
## [161] "66\t4\t0.0\t4\t3 1"
## [162] "67\t1\t0.0\t4\t1"
## [163] "69\t1\t0.0\t4\t0 1"
## [164] "72\t1\t0.0\t4\t1"
## [165] "73\t1\t0.0\t4\t1"
## [166] "74\t2\t0.0\t4\t1 1"
## [167] "75\t5\t0.0\t4\t4 1"
## [168] "77\t3\t0.0\t4\t3"
## [169] "78\t1\t0.0\t4\t1"
## [170] "79\t4\t0.0\t4\t3 0 1"
## [171] "81\t3\t0.0\t4\t3"
## [172] "82\t2\t0.0\t4\t2"
## [173] "83\t2\t0.0\t4\t2"
## [174] "84\t2\t0.0\t4\t2"
## [175] "85\t10\t0.0\t4\t9 0 0 0 1"
## [176] "86\t2\t0.0\t4\t2"
## [177] "87\t7\t0.0\t4\t7"
## [178] "88\t2\t0.0\t4\t1 1"
## [179] "89\t2\t0.0\t4\t2"
## [180] "90\t1\t0.0\t4\t1"
## [181] "91\t1\t0.0\t4\t1"
## [182] "92\t4\t0.0\t4\t4"
## [183] "93\t1\t0.0\t4\t1"
## [184] "94\t7\t0.0\t4\t5 2"
## [185] "95\t3\t0.0\t4\t3"
## [186] "96\t1\t0.0\t4\t0 1"
## [187] "97\t1\t0.0\t4\t1"
## [188] "98\t1\t0.0\t4\t1"
## [189] "99\t2\t0.0\t4\t2"
## [190] "101\t3\t0.0\t4\t2 1"
## [191] "102\t2\t0.0\t4\t2"
## [192] "103\t2\t0.0\t4\t2"
## [193] "104\t1\t0.0\t4\t1"
## [194] "105\t5\t0.0\t4\t5"
## [195] "106\t2\t0.0\t4\t2"
## [196] "108\t2\t0.0\t4\t2"
## [197] "109\t1\t0.0\t4\t1"
## [198] "110\t6\t0.0\t4\t6"
## [199] "116\t2\t0.0\t4\t2"
## [200] "117\t1\t0.0\t4\t1"
## [201] "118\t20\t0.0\t4\t16 4"
## [202] "119\t2\t0.0\t4\t2"
## [203] "121\t1\t0.0\t4\t1"
## [204] "122\t1\t0.0\t4\t1"
## [205] "125\t2\t0.0\t4\t2"
## [206] "126\t3\t0.0\t4\t3"
## [207] "127\t2\t0.0\t4\t2"
## [208] "128\t4\t0.0\t4\t4"
## [209] "129\t1\t0.0\t4\t1"
## [210] "132\t1\t0.0\t4\t1"
## [211] "134\t3\t0.0\t4\t2 1"
## [212] "136\t1\t0.0\t4\t1"
## [213] "137\t6\t0.0\t4\t6"
## [214] "138\t2\t0.0\t4\t2"
## [215] "141\t3\t0.0\t4\t3"
## [216] "142\t2\t0.0\t4\t1 1"
## [217] "144\t1\t0.0\t4\t1"
## [218] "145\t1\t0.0\t4\t1"
## [219] "146\t2\t0.0\t4\t1 1"
## [220] "147\t1\t0.0\t4\t1"
## [221] "150\t2\t0.0\t4\t2"
## [222] "151\t2\t0.0\t4\t2"
## [223] "152\t1\t0.0\t4\t1"
## [224] "159\t2\t0.0\t4\t2"
## [225] "160\t2\t0.0\t4\t2"
## [226] "161\t1\t0.0\t4\t1"
## [227] "162\t2\t0.0\t4\t2"
## [228] "165\t3\t0.0\t4\t3"
## [229] "166\t2\t0.0\t4\t2"
## [230] "171\t1\t0.0\t4\t1"
## [231] "173\t3\t0.0\t4\t3"
## [232] ""
## [233] ""
## [234] "WARNING:"
## [235] " One or more of your adapter sequences may be incomplete."
## [236] " Please see the detailed output above."
##
## [[51]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/55RNA3_S51_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/55RNA3_S51_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/55RNA3_S51_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/55RNA3_S51_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.90 s (116 us/read; 0.52 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 7,778"
## [9] " Read 1 with adapter: 170 (2.2%)"
## [10] " Read 2 with adapter: 499 (6.4%)"
## [11] "Pairs written (passing filters): 7,776 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,266,760 bp"
## [14] " Read 1: 1,524,488 bp"
## [15] " Read 2: 1,742,272 bp"
## [16] "Total written (filtered): 3,210,979 bp (98.3%)"
## [17] " Read 1: 1,510,586 bp"
## [18] " Read 2: 1,700,393 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 5 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "8\t1\t0.1\t0\t1"
## [30] "26\t1\t0.0\t2\t1"
## [31] "30\t1\t0.0\t3\t1"
## [32] "31\t1\t0.0\t3\t1"
## [33] "65\t1\t0.0\t4\t0 1"
## [34] ""
## [35] ""
## [36] "=== First read: Adapter 2 ==="
## [37] ""
## [38] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 165 times"
## [39] ""
## [40] "No. of allowed errors:"
## [41] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [42] ""
## [43] "Bases preceding removed adapters:"
## [44] " A: 2.4%"
## [45] " C: 1.8%"
## [46] " G: 95.2%"
## [47] " T: 0.6%"
## [48] " none/other: 0.0%"
## [49] "WARNING:"
## [50] " The adapter is preceded by \"G\" extremely often."
## [51] " The provided adapter sequence could be incomplete at its 3' end."
## [52] ""
## [53] "Overview of removed sequences"
## [54] "length\tcount\texpect\tmax.err\terror counts"
## [55] "10\t2\t0.0\t1\t2"
## [56] "15\t1\t0.0\t1\t1"
## [57] "16\t3\t0.0\t1\t2 1"
## [58] "17\t2\t0.0\t1\t2"
## [59] "23\t1\t0.0\t2\t1"
## [60] "25\t1\t0.0\t2\t0 1"
## [61] "26\t1\t0.0\t2\t1"
## [62] "36\t6\t0.0\t2\t6"
## [63] "42\t1\t0.0\t2\t1"
## [64] "43\t1\t0.0\t2\t1"
## [65] "49\t1\t0.0\t2\t1"
## [66] "56\t1\t0.0\t2\t1"
## [67] "60\t1\t0.0\t2\t1"
## [68] "64\t1\t0.0\t2\t1"
## [69] "66\t1\t0.0\t2\t1"
## [70] "81\t1\t0.0\t2\t1"
## [71] "82\t27\t0.0\t2\t27"
## [72] "90\t104\t0.0\t2\t103 1"
## [73] "91\t5\t0.0\t2\t4 1"
## [74] "109\t2\t0.0\t2\t2"
## [75] "110\t1\t0.0\t2\t1"
## [76] "125\t1\t0.0\t2\t1"
## [77] ""
## [78] ""
## [79] "=== Second read: Adapter 3 ==="
## [80] ""
## [81] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 2 times"
## [82] ""
## [83] "No. of allowed errors:"
## [84] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [85] ""
## [86] "Overview of removed sequences"
## [87] "length\tcount\texpect\tmax.err\terror counts"
## [88] "5\t2\t7.6\t0\t2"
## [89] ""
## [90] ""
## [91] "=== Second read: Adapter 4 ==="
## [92] ""
## [93] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 499 times"
## [94] ""
## [95] "No. of allowed errors:"
## [96] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [97] ""
## [98] "Bases preceding removed adapters:"
## [99] " A: 91.6%"
## [100] " C: 6.0%"
## [101] " G: 0.8%"
## [102] " T: 1.6%"
## [103] " none/other: 0.0%"
## [104] "WARNING:"
## [105] " The adapter is preceded by \"A\" extremely often."
## [106] " The provided adapter sequence could be incomplete at its 3' end."
## [107] ""
## [108] "Overview of removed sequences"
## [109] "length\tcount\texpect\tmax.err\terror counts"
## [110] "5\t3\t7.6\t0\t3"
## [111] "6\t3\t1.9\t0\t3"
## [112] "8\t3\t0.1\t0\t3"
## [113] "10\t1\t0.0\t1\t1"
## [114] "11\t1\t0.0\t1\t1"
## [115] "12\t1\t0.0\t1\t1"
## [116] "14\t6\t0.0\t1\t5 1"
## [117] "15\t5\t0.0\t1\t5"
## [118] "16\t4\t0.0\t1\t4"
## [119] "17\t5\t0.0\t1\t4 1"
## [120] "18\t1\t0.0\t1\t1"
## [121] "19\t2\t0.0\t1\t2"
## [122] "20\t3\t0.0\t2\t3"
## [123] "21\t1\t0.0\t2\t1"
## [124] "22\t1\t0.0\t2\t1"
## [125] "23\t5\t0.0\t2\t4 1"
## [126] "24\t3\t0.0\t2\t2 0 1"
## [127] "25\t2\t0.0\t2\t2"
## [128] "26\t5\t0.0\t2\t3 2"
## [129] "27\t7\t0.0\t2\t6 1"
## [130] "28\t1\t0.0\t2\t1"
## [131] "30\t1\t0.0\t3\t1"
## [132] "31\t1\t0.0\t3\t1"
## [133] "32\t1\t0.0\t3\t1"
## [134] "33\t5\t0.0\t3\t4 0 1"
## [135] "34\t3\t0.0\t3\t2 0 1"
## [136] "35\t6\t0.0\t3\t5 1"
## [137] "36\t2\t0.0\t3\t1 1"
## [138] "38\t6\t0.0\t3\t3 2 0 1"
## [139] "39\t2\t0.0\t3\t1 1"
## [140] "42\t1\t0.0\t4\t1"
## [141] "43\t3\t0.0\t4\t2 1"
## [142] "44\t7\t0.0\t4\t2 4 1"
## [143] "45\t3\t0.0\t4\t2 1"
## [144] "46\t3\t0.0\t4\t2 1"
## [145] "47\t6\t0.0\t4\t4 2"
## [146] "48\t2\t0.0\t4\t2"
## [147] "49\t1\t0.0\t4\t1"
## [148] "50\t4\t0.0\t4\t3 0 0 1"
## [149] "51\t5\t0.0\t4\t3 1 1"
## [150] "52\t8\t0.0\t4\t6 1 0 0 1"
## [151] "53\t6\t0.0\t4\t5 0 1"
## [152] "54\t2\t0.0\t4\t2"
## [153] "55\t4\t0.0\t4\t3 0 1"
## [154] "56\t1\t0.0\t4\t1"
## [155] "57\t7\t0.0\t4\t7"
## [156] "58\t5\t0.0\t4\t3 1 0 1"
## [157] "59\t6\t0.0\t4\t5 1"
## [158] "62\t1\t0.0\t4\t1"
## [159] "63\t1\t0.0\t4\t1"
## [160] "64\t10\t0.0\t4\t9 1"
## [161] "65\t5\t0.0\t4\t3 2"
## [162] "66\t3\t0.0\t4\t3"
## [163] "67\t2\t0.0\t4\t2"
## [164] "68\t2\t0.0\t4\t2"
## [165] "69\t1\t0.0\t4\t1"
## [166] "70\t1\t0.0\t4\t1"
## [167] "71\t4\t0.0\t4\t4"
## [168] "72\t3\t0.0\t4\t3"
## [169] "73\t3\t0.0\t4\t3"
## [170] "74\t2\t0.0\t4\t2"
## [171] "75\t1\t0.0\t4\t1"
## [172] "76\t2\t0.0\t4\t2"
## [173] "77\t3\t0.0\t4\t2 1"
## [174] "78\t2\t0.0\t4\t2"
## [175] "79\t5\t0.0\t4\t5"
## [176] "82\t2\t0.0\t4\t2"
## [177] "83\t1\t0.0\t4\t1"
## [178] "84\t3\t0.0\t4\t2 1"
## [179] "85\t5\t0.0\t4\t5"
## [180] "86\t11\t0.0\t4\t10 1"
## [181] "87\t4\t0.0\t4\t4"
## [182] "88\t1\t0.0\t4\t0 1"
## [183] "89\t3\t0.0\t4\t2 1"
## [184] "90\t1\t0.0\t4\t1"
## [185] "92\t2\t0.0\t4\t2"
## [186] "93\t1\t0.0\t4\t1"
## [187] "94\t15\t0.0\t4\t15"
## [188] "95\t1\t0.0\t4\t1"
## [189] "96\t2\t0.0\t4\t2"
## [190] "97\t1\t0.0\t4\t1"
## [191] "98\t3\t0.0\t4\t3"
## [192] "99\t3\t0.0\t4\t3"
## [193] "100\t3\t0.0\t4\t3"
## [194] "101\t3\t0.0\t4\t2 1"
## [195] "103\t3\t0.0\t4\t3"
## [196] "104\t7\t0.0\t4\t5 2"
## [197] "105\t1\t0.0\t4\t1"
## [198] "106\t5\t0.0\t4\t5"
## [199] "107\t3\t0.0\t4\t3"
## [200] "108\t2\t0.0\t4\t2"
## [201] "109\t2\t0.0\t4\t2"
## [202] "110\t28\t0.0\t4\t28"
## [203] "112\t3\t0.0\t4\t3"
## [204] "113\t4\t0.0\t4\t4"
## [205] "114\t1\t0.0\t4\t1"
## [206] "115\t2\t0.0\t4\t2"
## [207] "116\t1\t0.0\t4\t1"
## [208] "117\t1\t0.0\t4\t1"
## [209] "118\t106\t0.0\t4\t98 7 1"
## [210] "119\t3\t0.0\t4\t1 2"
## [211] "120\t1\t0.0\t4\t1"
## [212] "121\t3\t0.0\t4\t3"
## [213] "127\t4\t0.0\t4\t3 1"
## [214] "128\t3\t0.0\t4\t2 1"
## [215] "129\t1\t0.0\t4\t1"
## [216] "130\t2\t0.0\t4\t2"
## [217] "131\t1\t0.0\t4\t1"
## [218] "132\t1\t0.0\t4\t1"
## [219] "134\t3\t0.0\t4\t2 1"
## [220] "136\t1\t0.0\t4\t1"
## [221] "137\t3\t0.0\t4\t3"
## [222] "138\t3\t0.0\t4\t3"
## [223] "139\t2\t0.0\t4\t2"
## [224] "144\t3\t0.0\t4\t3"
## [225] "145\t1\t0.0\t4\t1"
## [226] "146\t1\t0.0\t4\t1"
## [227] "147\t1\t0.0\t4\t1"
## [228] "150\t1\t0.0\t4\t1"
## [229] "153\t3\t0.0\t4\t3"
## [230] "158\t1\t0.0\t4\t1"
## [231] "160\t1\t0.0\t4\t1"
## [232] "161\t1\t0.0\t4\t1"
## [233] "165\t1\t0.0\t4\t1"
## [234] "167\t1\t0.0\t4\t1"
## [235] "168\t1\t0.0\t4\t1"
## [236] "173\t1\t0.0\t4\t1"
## [237] "175\t1\t0.0\t4\t1"
## [238] "179\t1\t0.0\t4\t1"
## [239] ""
## [240] ""
## [241] "WARNING:"
## [242] " One or more of your adapter sequences may be incomplete."
## [243] " Please see the detailed output above."
##
## [[52]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/55RNA4_S52_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/55RNA4_S52_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/55RNA4_S52_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/55RNA4_S52_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.25 s (117 us/read; 0.51 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 2,165"
## [9] " Read 1 with adapter: 11 (0.5%)"
## [10] " Read 2 with adapter: 86 (4.0%)"
## [11] "Pairs written (passing filters): 2,164 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 909,300 bp"
## [14] " Read 1: 424,340 bp"
## [15] " Read 2: 484,960 bp"
## [16] "Total written (filtered): 902,063 bp (99.2%)"
## [17] " Read 1: 423,498 bp"
## [18] " Read 2: 478,565 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 11 times"
## [27] ""
## [28] "No. of allowed errors:"
## [29] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [30] ""
## [31] "Bases preceding removed adapters:"
## [32] " A: 18.2%"
## [33] " C: 9.1%"
## [34] " G: 72.7%"
## [35] " T: 0.0%"
## [36] " none/other: 0.0%"
## [37] ""
## [38] "Overview of removed sequences"
## [39] "length\tcount\texpect\tmax.err\terror counts"
## [40] "15\t1\t0.0\t1\t1"
## [41] "17\t1\t0.0\t1\t1"
## [42] "25\t1\t0.0\t2\t1"
## [43] "36\t1\t0.0\t2\t1"
## [44] "82\t1\t0.0\t2\t1"
## [45] "90\t4\t0.0\t2\t4"
## [46] "111\t1\t0.0\t2\t1"
## [47] "147\t1\t0.0\t2\t1"
## [48] ""
## [49] ""
## [50] "=== Second read: Adapter 3 ==="
## [51] ""
## [52] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [53] ""
## [54] "No. of allowed errors:"
## [55] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [56] ""
## [57] "Overview of removed sequences"
## [58] "length\tcount\texpect\tmax.err\terror counts"
## [59] "5\t1\t2.1\t0\t1"
## [60] ""
## [61] ""
## [62] "=== Second read: Adapter 4 ==="
## [63] ""
## [64] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 86 times"
## [65] ""
## [66] "No. of allowed errors:"
## [67] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [68] ""
## [69] "Bases preceding removed adapters:"
## [70] " A: 88.4%"
## [71] " C: 7.0%"
## [72] " G: 4.7%"
## [73] " T: 0.0%"
## [74] " none/other: 0.0%"
## [75] "WARNING:"
## [76] " The adapter is preceded by \"A\" extremely often."
## [77] " The provided adapter sequence could be incomplete at its 3' end."
## [78] ""
## [79] "Overview of removed sequences"
## [80] "length\tcount\texpect\tmax.err\terror counts"
## [81] "6\t2\t0.5\t0\t2"
## [82] "8\t1\t0.0\t0\t1"
## [83] "12\t1\t0.0\t1\t1"
## [84] "13\t2\t0.0\t1\t2"
## [85] "24\t1\t0.0\t2\t1"
## [86] "26\t1\t0.0\t2\t0 1"
## [87] "31\t1\t0.0\t3\t0 0 1"
## [88] "34\t1\t0.0\t3\t1"
## [89] "35\t2\t0.0\t3\t1 0 1"
## [90] "40\t1\t0.0\t4\t1"
## [91] "42\t1\t0.0\t4\t1"
## [92] "43\t2\t0.0\t4\t1 1"
## [93] "45\t1\t0.0\t4\t1"
## [94] "46\t1\t0.0\t4\t0 1"
## [95] "50\t1\t0.0\t4\t1"
## [96] "51\t3\t0.0\t4\t3"
## [97] "52\t3\t0.0\t4\t3"
## [98] "53\t1\t0.0\t4\t0 0 1"
## [99] "55\t2\t0.0\t4\t1 1"
## [100] "58\t1\t0.0\t4\t1"
## [101] "60\t1\t0.0\t4\t1"
## [102] "61\t1\t0.0\t4\t0 1"
## [103] "62\t3\t0.0\t4\t2 1"
## [104] "63\t2\t0.0\t4\t2"
## [105] "64\t2\t0.0\t4\t2"
## [106] "65\t1\t0.0\t4\t1"
## [107] "66\t2\t0.0\t4\t2"
## [108] "68\t1\t0.0\t4\t1"
## [109] "69\t3\t0.0\t4\t2 0 0 1"
## [110] "70\t1\t0.0\t4\t1"
## [111] "71\t1\t0.0\t4\t1"
## [112] "72\t1\t0.0\t4\t1"
## [113] "73\t1\t0.0\t4\t0 1"
## [114] "77\t2\t0.0\t4\t2"
## [115] "79\t1\t0.0\t4\t1"
## [116] "81\t1\t0.0\t4\t1"
## [117] "84\t1\t0.0\t4\t1"
## [118] "86\t1\t0.0\t4\t1"
## [119] "87\t1\t0.0\t4\t1"
## [120] "88\t4\t0.0\t4\t3 0 1"
## [121] "92\t1\t0.0\t4\t1"
## [122] "93\t2\t0.0\t4\t2"
## [123] "94\t1\t0.0\t4\t1"
## [124] "95\t1\t0.0\t4\t1"
## [125] "98\t1\t0.0\t4\t1"
## [126] "102\t2\t0.0\t4\t1 1"
## [127] "104\t2\t0.0\t4\t2"
## [128] "106\t1\t0.0\t4\t1"
## [129] "110\t2\t0.0\t4\t1 1"
## [130] "113\t1\t0.0\t4\t1"
## [131] "115\t1\t0.0\t4\t1"
## [132] "118\t4\t0.0\t4\t4"
## [133] "121\t1\t0.0\t4\t1"
## [134] "133\t1\t0.0\t4\t1"
## [135] "136\t1\t0.0\t4\t0 0 1"
## [136] "139\t1\t0.0\t4\t1"
## [137] "146\t1\t0.0\t4\t1"
## [138] "164\t1\t0.0\t4\t1"
## [139] "175\t1\t0.0\t4\t1"
## [140] ""
## [141] ""
## [142] "WARNING:"
## [143] " One or more of your adapter sequences may be incomplete."
## [144] " Please see the detailed output above."
##
## [[53]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/71A1_S53_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/71A1_S53_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/71A1_S53_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/71A1_S53_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.92 s (107 us/read; 0.56 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 17,921"
## [9] " Read 1 with adapter: 3 (0.0%)"
## [10] " Read 2 with adapter: 132 (0.7%)"
## [11] "Pairs written (passing filters): 17,921 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 7,526,820 bp"
## [14] " Read 1: 3,512,516 bp"
## [15] " Read 2: 4,014,304 bp"
## [16] "Total written (filtered): 7,518,914 bp (99.9%)"
## [17] " Read 1: 3,512,468 bp"
## [18] " Read 2: 4,006,446 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t17.5\t0\t1"
## [30] "7\t1\t1.1\t0\t1"
## [31] "36\t1\t0.0\t3\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 0 times"
## [37] ""
## [38] "=== Second read: Adapter 3 ==="
## [39] ""
## [40] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 2 times"
## [41] ""
## [42] "No. of allowed errors:"
## [43] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [44] ""
## [45] "Overview of removed sequences"
## [46] "length\tcount\texpect\tmax.err\terror counts"
## [47] "12\t1\t0.0\t1\t1"
## [48] "14\t1\t0.0\t1\t0 1"
## [49] ""
## [50] ""
## [51] "=== Second read: Adapter 4 ==="
## [52] ""
## [53] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 130 times"
## [54] ""
## [55] "No. of allowed errors:"
## [56] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [57] ""
## [58] "Bases preceding removed adapters:"
## [59] " A: 62.3%"
## [60] " C: 36.2%"
## [61] " G: 1.5%"
## [62] " T: 0.0%"
## [63] " none/other: 0.0%"
## [64] ""
## [65] "Overview of removed sequences"
## [66] "length\tcount\texpect\tmax.err\terror counts"
## [67] "5\t3\t17.5\t0\t3"
## [68] "6\t1\t4.4\t0\t1"
## [69] "7\t1\t1.1\t0\t1"
## [70] "9\t5\t0.1\t0\t5"
## [71] "10\t1\t0.0\t1\t1"
## [72] "11\t1\t0.0\t1\t1"
## [73] "12\t1\t0.0\t1\t1"
## [74] "14\t4\t0.0\t1\t4"
## [75] "15\t1\t0.0\t1\t1"
## [76] "16\t5\t0.0\t1\t5"
## [77] "17\t4\t0.0\t1\t3 1"
## [78] "18\t2\t0.0\t1\t2"
## [79] "21\t1\t0.0\t2\t1"
## [80] "22\t4\t0.0\t2\t3 1"
## [81] "25\t2\t0.0\t2\t2"
## [82] "28\t1\t0.0\t2\t1"
## [83] "32\t1\t0.0\t3\t1"
## [84] "33\t1\t0.0\t3\t1"
## [85] "34\t5\t0.0\t3\t5"
## [86] "35\t3\t0.0\t3\t2 1"
## [87] "38\t2\t0.0\t3\t2"
## [88] "39\t1\t0.0\t3\t1"
## [89] "40\t1\t0.0\t4\t1"
## [90] "41\t1\t0.0\t4\t1"
## [91] "42\t1\t0.0\t4\t0 0 1"
## [92] "44\t3\t0.0\t4\t2 1"
## [93] "45\t2\t0.0\t4\t2"
## [94] "46\t2\t0.0\t4\t2"
## [95] "48\t1\t0.0\t4\t1"
## [96] "52\t2\t0.0\t4\t2"
## [97] "53\t1\t0.0\t4\t1"
## [98] "54\t1\t0.0\t4\t1"
## [99] "55\t1\t0.0\t4\t1"
## [100] "57\t2\t0.0\t4\t2"
## [101] "58\t3\t0.0\t4\t2 1"
## [102] "59\t1\t0.0\t4\t1"
## [103] "65\t2\t0.0\t4\t2"
## [104] "66\t1\t0.0\t4\t1"
## [105] "69\t1\t0.0\t4\t1"
## [106] "71\t1\t0.0\t4\t1"
## [107] "72\t3\t0.0\t4\t3"
## [108] "73\t3\t0.0\t4\t3"
## [109] "74\t2\t0.0\t4\t2"
## [110] "75\t1\t0.0\t4\t1"
## [111] "76\t1\t0.0\t4\t1"
## [112] "77\t1\t0.0\t4\t1"
## [113] "79\t2\t0.0\t4\t1 1"
## [114] "81\t2\t0.0\t4\t2"
## [115] "82\t1\t0.0\t4\t1"
## [116] "84\t2\t0.0\t4\t2"
## [117] "85\t1\t0.0\t4\t0 1"
## [118] "86\t2\t0.0\t4\t2"
## [119] "87\t2\t0.0\t4\t2"
## [120] "88\t1\t0.0\t4\t1"
## [121] "89\t1\t0.0\t4\t1"
## [122] "93\t2\t0.0\t4\t2"
## [123] "97\t1\t0.0\t4\t1"
## [124] "98\t1\t0.0\t4\t1"
## [125] "99\t1\t0.0\t4\t1"
## [126] "103\t1\t0.0\t4\t1"
## [127] "106\t1\t0.0\t4\t1"
## [128] "107\t1\t0.0\t4\t1"
## [129] "109\t1\t0.0\t4\t1"
## [130] "111\t2\t0.0\t4\t2"
## [131] "112\t1\t0.0\t4\t1"
## [132] "113\t1\t0.0\t4\t1"
## [133] "114\t2\t0.0\t4\t1 1"
## [134] "116\t1\t0.0\t4\t1"
## [135] "121\t1\t0.0\t4\t1"
## [136] "129\t1\t0.0\t4\t1"
## [137] "131\t2\t0.0\t4\t2"
## [138] "138\t1\t0.0\t4\t1"
## [139] "140\t2\t0.0\t4\t2"
## [140] "145\t1\t0.0\t4\t1"
## [141] "147\t1\t0.0\t4\t1"
## [142] "157\t1\t0.0\t4\t1"
## [143] "160\t1\t0.0\t4\t1"
## [144] "171\t1\t0.0\t4\t1"
##
## [[54]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/71A2_S54_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/71A2_S54_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/71A2_S54_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/71A2_S54_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 2.27 s (109 us/read; 0.55 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 20,847"
## [9] " Read 1 with adapter: 8 (0.0%)"
## [10] " Read 2 with adapter: 185 (0.9%)"
## [11] "Pairs written (passing filters): 20,846 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 8,755,740 bp"
## [14] " Read 1: 4,086,012 bp"
## [15] " Read 2: 4,669,728 bp"
## [16] "Total written (filtered): 8,743,381 bp (99.9%)"
## [17] " Read 1: 4,085,693 bp"
## [18] " Read 2: 4,657,688 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 6 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "7\t1\t1.3\t0\t1"
## [30] "8\t3\t0.3\t0\t3"
## [31] "9\t1\t0.1\t0\t1"
## [32] "24\t1\t0.0\t2\t1"
## [33] ""
## [34] ""
## [35] "=== First read: Adapter 2 ==="
## [36] ""
## [37] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 2 times"
## [38] ""
## [39] "No. of allowed errors:"
## [40] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [41] ""
## [42] "Bases preceding removed adapters:"
## [43] " A: 0.0%"
## [44] " C: 0.0%"
## [45] " G: 100.0%"
## [46] " T: 0.0%"
## [47] " none/other: 0.0%"
## [48] ""
## [49] "Overview of removed sequences"
## [50] "length\tcount\texpect\tmax.err\terror counts"
## [51] "24\t1\t0.0\t2\t1"
## [52] "35\t1\t0.0\t2\t1"
## [53] ""
## [54] ""
## [55] "=== Second read: Adapter 3 ==="
## [56] ""
## [57] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [58] ""
## [59] "No. of allowed errors:"
## [60] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [61] ""
## [62] "Overview of removed sequences"
## [63] "length\tcount\texpect\tmax.err\terror counts"
## [64] "7\t1\t1.3\t0\t1"
## [65] ""
## [66] ""
## [67] "=== Second read: Adapter 4 ==="
## [68] ""
## [69] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 184 times"
## [70] ""
## [71] "No. of allowed errors:"
## [72] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [73] ""
## [74] "Bases preceding removed adapters:"
## [75] " A: 62.0%"
## [76] " C: 36.4%"
## [77] " G: 1.1%"
## [78] " T: 0.5%"
## [79] " none/other: 0.0%"
## [80] ""
## [81] "Overview of removed sequences"
## [82] "length\tcount\texpect\tmax.err\terror counts"
## [83] "5\t6\t20.4\t0\t6"
## [84] "6\t3\t5.1\t0\t3"
## [85] "7\t2\t1.3\t0\t2"
## [86] "8\t3\t0.3\t0\t3"
## [87] "10\t1\t0.0\t1\t1"
## [88] "11\t2\t0.0\t1\t2"
## [89] "12\t4\t0.0\t1\t3 1"
## [90] "14\t1\t0.0\t1\t1"
## [91] "15\t1\t0.0\t1\t1"
## [92] "16\t2\t0.0\t1\t1 1"
## [93] "17\t2\t0.0\t1\t2"
## [94] "18\t4\t0.0\t1\t3 1"
## [95] "19\t1\t0.0\t1\t1"
## [96] "20\t1\t0.0\t2\t1"
## [97] "21\t1\t0.0\t2\t1"
## [98] "22\t3\t0.0\t2\t3"
## [99] "23\t1\t0.0\t2\t0 1"
## [100] "24\t4\t0.0\t2\t2 2"
## [101] "25\t4\t0.0\t2\t3 1"
## [102] "27\t2\t0.0\t2\t2"
## [103] "28\t2\t0.0\t2\t1 1"
## [104] "29\t1\t0.0\t2\t1"
## [105] "30\t1\t0.0\t3\t0 0 0 1"
## [106] "31\t2\t0.0\t3\t2"
## [107] "32\t3\t0.0\t3\t3"
## [108] "33\t2\t0.0\t3\t2"
## [109] "34\t1\t0.0\t3\t0 1"
## [110] "35\t2\t0.0\t3\t2"
## [111] "37\t1\t0.0\t3\t0 1"
## [112] "38\t2\t0.0\t3\t1 1"
## [113] "39\t1\t0.0\t3\t1"
## [114] "41\t3\t0.0\t4\t3"
## [115] "42\t1\t0.0\t4\t0 1"
## [116] "43\t3\t0.0\t4\t3"
## [117] "45\t3\t0.0\t4\t2 1"
## [118] "46\t1\t0.0\t4\t1"
## [119] "47\t2\t0.0\t4\t2"
## [120] "48\t1\t0.0\t4\t1"
## [121] "50\t1\t0.0\t4\t1"
## [122] "51\t4\t0.0\t4\t3 1"
## [123] "53\t1\t0.0\t4\t1"
## [124] "54\t1\t0.0\t4\t1"
## [125] "55\t1\t0.0\t4\t1"
## [126] "56\t1\t0.0\t4\t1"
## [127] "57\t1\t0.0\t4\t1"
## [128] "58\t1\t0.0\t4\t1"
## [129] "60\t1\t0.0\t4\t1"
## [130] "62\t1\t0.0\t4\t1"
## [131] "63\t2\t0.0\t4\t2"
## [132] "64\t4\t0.0\t4\t4"
## [133] "65\t1\t0.0\t4\t1"
## [134] "72\t3\t0.0\t4\t1 2"
## [135] "74\t4\t0.0\t4\t4"
## [136] "75\t2\t0.0\t4\t1 0 0 1"
## [137] "77\t2\t0.0\t4\t1 1"
## [138] "79\t3\t0.0\t4\t1 1 0 0 1"
## [139] "80\t1\t0.0\t4\t1"
## [140] "81\t1\t0.0\t4\t1"
## [141] "82\t1\t0.0\t4\t1"
## [142] "83\t1\t0.0\t4\t1"
## [143] "84\t4\t0.0\t4\t4"
## [144] "86\t2\t0.0\t4\t2"
## [145] "89\t2\t0.0\t4\t2"
## [146] "90\t2\t0.0\t4\t2"
## [147] "92\t2\t0.0\t4\t1 1"
## [148] "94\t2\t0.0\t4\t1 1"
## [149] "95\t1\t0.0\t4\t1"
## [150] "96\t1\t0.0\t4\t1"
## [151] "97\t2\t0.0\t4\t2"
## [152] "99\t2\t0.0\t4\t2"
## [153] "101\t3\t0.0\t4\t3"
## [154] "102\t1\t0.0\t4\t1"
## [155] "104\t1\t0.0\t4\t1"
## [156] "105\t2\t0.0\t4\t2"
## [157] "106\t1\t0.0\t4\t1"
## [158] "108\t4\t0.0\t4\t3 1"
## [159] "109\t1\t0.0\t4\t1"
## [160] "111\t3\t0.0\t4\t3"
## [161] "114\t1\t0.0\t4\t1"
## [162] "115\t2\t0.0\t4\t2"
## [163] "116\t1\t0.0\t4\t1"
## [164] "117\t2\t0.0\t4\t1 1"
## [165] "118\t2\t0.0\t4\t1 1"
## [166] "119\t3\t0.0\t4\t3"
## [167] "120\t1\t0.0\t4\t1"
## [168] "121\t1\t0.0\t4\t1"
## [169] "125\t1\t0.0\t4\t1"
## [170] "131\t2\t0.0\t4\t2"
## [171] "134\t1\t0.0\t4\t1"
## [172] "136\t1\t0.0\t4\t1"
## [173] "138\t1\t0.0\t4\t1"
## [174] "139\t1\t0.0\t4\t0 1"
## [175] "140\t1\t0.0\t4\t1"
## [176] "141\t1\t0.0\t4\t1"
## [177] "146\t2\t0.0\t4\t2"
## [178] "147\t1\t0.0\t4\t1"
## [179] "150\t1\t0.0\t4\t1"
## [180] "158\t1\t0.0\t4\t1"
## [181] "160\t2\t0.0\t4\t2"
## [182] "177\t1\t0.0\t4\t1"
##
## [[55]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/71A3_S55_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/71A3_S55_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/71A3_S55_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/71A3_S55_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.72 s (106 us/read; 0.57 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 16,250"
## [9] " Read 1 with adapter: 18 (0.1%)"
## [10] " Read 2 with adapter: 120 (0.7%)"
## [11] "Pairs written (passing filters): 16,249 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 6,825,000 bp"
## [14] " Read 1: 3,185,000 bp"
## [15] " Read 2: 3,640,000 bp"
## [16] "Total written (filtered): 6,815,488 bp (99.9%)"
## [17] " Read 1: 3,183,427 bp"
## [18] " Read 2: 3,632,061 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 3 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "14\t1\t0.0\t1\t1"
## [30] "17\t1\t0.0\t1\t1"
## [31] "21\t1\t0.0\t2\t1"
## [32] ""
## [33] ""
## [34] "=== First read: Adapter 2 ==="
## [35] ""
## [36] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 15 times"
## [37] ""
## [38] "No. of allowed errors:"
## [39] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [40] ""
## [41] "Bases preceding removed adapters:"
## [42] " A: 6.7%"
## [43] " C: 40.0%"
## [44] " G: 53.3%"
## [45] " T: 0.0%"
## [46] " none/other: 0.0%"
## [47] ""
## [48] "Overview of removed sequences"
## [49] "length\tcount\texpect\tmax.err\terror counts"
## [50] "52\t6\t0.0\t2\t6"
## [51] "61\t1\t0.0\t2\t1"
## [52] "104\t2\t0.0\t2\t2"
## [53] "124\t6\t0.0\t2\t6"
## [54] ""
## [55] ""
## [56] "=== Second read: Adapter 3 ==="
## [57] ""
## [58] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [59] ""
## [60] "=== Second read: Adapter 4 ==="
## [61] ""
## [62] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 120 times"
## [63] ""
## [64] "No. of allowed errors:"
## [65] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [66] ""
## [67] "Bases preceding removed adapters:"
## [68] " A: 50.0%"
## [69] " C: 41.7%"
## [70] " G: 5.8%"
## [71] " T: 2.5%"
## [72] " none/other: 0.0%"
## [73] ""
## [74] "Overview of removed sequences"
## [75] "length\tcount\texpect\tmax.err\terror counts"
## [76] "5\t1\t15.9\t0\t1"
## [77] "6\t1\t4.0\t0\t1"
## [78] "7\t1\t1.0\t0\t1"
## [79] "8\t3\t0.2\t0\t3"
## [80] "9\t1\t0.1\t0\t1"
## [81] "10\t1\t0.0\t1\t1"
## [82] "11\t1\t0.0\t1\t0 1"
## [83] "12\t1\t0.0\t1\t1"
## [84] "13\t3\t0.0\t1\t3"
## [85] "15\t1\t0.0\t1\t1"
## [86] "16\t2\t0.0\t1\t2"
## [87] "17\t1\t0.0\t1\t1"
## [88] "19\t1\t0.0\t1\t1"
## [89] "20\t2\t0.0\t2\t2"
## [90] "21\t1\t0.0\t2\t1"
## [91] "22\t1\t0.0\t2\t1"
## [92] "25\t1\t0.0\t2\t1"
## [93] "28\t1\t0.0\t2\t0 1"
## [94] "29\t1\t0.0\t2\t1"
## [95] "31\t1\t0.0\t3\t1"
## [96] "32\t4\t0.0\t3\t3 0 1"
## [97] "33\t1\t0.0\t3\t1"
## [98] "35\t3\t0.0\t3\t3"
## [99] "36\t1\t0.0\t3\t1"
## [100] "38\t1\t0.0\t3\t1"
## [101] "39\t5\t0.0\t3\t4 1"
## [102] "40\t1\t0.0\t4\t1"
## [103] "41\t3\t0.0\t4\t3"
## [104] "42\t2\t0.0\t4\t0 1 1"
## [105] "43\t1\t0.0\t4\t1"
## [106] "44\t2\t0.0\t4\t2"
## [107] "47\t1\t0.0\t4\t1"
## [108] "48\t1\t0.0\t4\t1"
## [109] "51\t1\t0.0\t4\t0 1"
## [110] "52\t1\t0.0\t4\t0 1"
## [111] "54\t1\t0.0\t4\t1"
## [112] "57\t2\t0.0\t4\t2"
## [113] "59\t1\t0.0\t4\t1"
## [114] "60\t3\t0.0\t4\t2 1"
## [115] "62\t1\t0.0\t4\t1"
## [116] "63\t1\t0.0\t4\t1"
## [117] "65\t1\t0.0\t4\t1"
## [118] "69\t2\t0.0\t4\t1 1"
## [119] "70\t2\t0.0\t4\t2"
## [120] "71\t2\t0.0\t4\t2"
## [121] "72\t1\t0.0\t4\t1"
## [122] "77\t1\t0.0\t4\t1"
## [123] "78\t2\t0.0\t4\t2"
## [124] "80\t7\t0.0\t4\t6 0 1"
## [125] "82\t1\t0.0\t4\t1"
## [126] "83\t1\t0.0\t4\t1"
## [127] "88\t3\t0.0\t4\t2 1"
## [128] "89\t3\t0.0\t4\t2 1"
## [129] "92\t1\t0.0\t4\t1"
## [130] "96\t1\t0.0\t4\t1"
## [131] "97\t1\t0.0\t4\t1"
## [132] "99\t1\t0.0\t4\t1"
## [133] "100\t2\t0.0\t4\t2"
## [134] "102\t1\t0.0\t4\t1"
## [135] "103\t1\t0.0\t4\t0 1"
## [136] "104\t1\t0.0\t4\t1"
## [137] "105\t1\t0.0\t4\t1"
## [138] "106\t1\t0.0\t4\t1"
## [139] "108\t1\t0.0\t4\t0 1"
## [140] "109\t1\t0.0\t4\t1"
## [141] "110\t1\t0.0\t4\t1"
## [142] "111\t1\t0.0\t4\t1"
## [143] "117\t1\t0.0\t4\t1"
## [144] "119\t1\t0.0\t4\t1"
## [145] "120\t1\t0.0\t4\t1"
## [146] "123\t1\t0.0\t4\t1"
## [147] "129\t1\t0.0\t4\t1"
## [148] "132\t2\t0.0\t4\t1 1"
## [149] "138\t1\t0.0\t4\t1"
## [150] "152\t6\t0.0\t4\t6"
## [151] "160\t1\t0.0\t4\t1"
## [152] "181\t1\t0.0\t4\t1"
##
## [[56]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/71ARNA1_S56_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/71ARNA1_S56_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/71ARNA1_S56_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/71ARNA1_S56_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.79 s (111 us/read; 0.54 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 7,101"
## [9] " Read 1 with adapter: 20 (0.3%)"
## [10] " Read 2 with adapter: 164 (2.3%)"
## [11] "Pairs written (passing filters): 7,100 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 2,982,420 bp"
## [14] " Read 1: 1,391,796 bp"
## [15] " Read 2: 1,590,624 bp"
## [16] "Total written (filtered): 2,969,324 bp (99.6%)"
## [17] " Read 1: 1,390,314 bp"
## [18] " Read 2: 1,579,010 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 2 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "6\t1\t1.7\t0\t1"
## [30] "10\t1\t0.0\t1\t0 1"
## [31] ""
## [32] ""
## [33] "=== First read: Adapter 2 ==="
## [34] ""
## [35] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 18 times"
## [36] ""
## [37] "No. of allowed errors:"
## [38] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [39] ""
## [40] "Bases preceding removed adapters:"
## [41] " A: 11.1%"
## [42] " C: 0.0%"
## [43] " G: 88.9%"
## [44] " T: 0.0%"
## [45] " none/other: 0.0%"
## [46] ""
## [47] "Overview of removed sequences"
## [48] "length\tcount\texpect\tmax.err\terror counts"
## [49] "10\t1\t0.0\t1\t1"
## [50] "16\t1\t0.0\t1\t1"
## [51] "24\t1\t0.0\t2\t1"
## [52] "36\t1\t0.0\t2\t1"
## [53] "59\t1\t0.0\t2\t1"
## [54] "61\t3\t0.0\t2\t3"
## [55] "73\t1\t0.0\t2\t1"
## [56] "83\t1\t0.0\t2\t1"
## [57] "90\t4\t0.0\t2\t4"
## [58] "142\t3\t0.0\t2\t3"
## [59] "158\t1\t0.0\t2\t1"
## [60] ""
## [61] ""
## [62] "=== Second read: Adapter 3 ==="
## [63] ""
## [64] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [65] ""
## [66] "No. of allowed errors:"
## [67] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [68] ""
## [69] "Overview of removed sequences"
## [70] "length\tcount\texpect\tmax.err\terror counts"
## [71] "5\t1\t6.9\t0\t1"
## [72] ""
## [73] ""
## [74] "=== Second read: Adapter 4 ==="
## [75] ""
## [76] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 163 times"
## [77] ""
## [78] "No. of allowed errors:"
## [79] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [80] ""
## [81] "Bases preceding removed adapters:"
## [82] " A: 76.7%"
## [83] " C: 17.8%"
## [84] " G: 4.9%"
## [85] " T: 0.6%"
## [86] " none/other: 0.0%"
## [87] ""
## [88] "Overview of removed sequences"
## [89] "length\tcount\texpect\tmax.err\terror counts"
## [90] "7\t2\t0.4\t0\t2"
## [91] "8\t1\t0.1\t0\t1"
## [92] "9\t3\t0.0\t0\t3"
## [93] "10\t2\t0.0\t1\t1 1"
## [94] "12\t1\t0.0\t1\t0 1"
## [95] "14\t2\t0.0\t1\t1 1"
## [96] "15\t1\t0.0\t1\t1"
## [97] "16\t1\t0.0\t1\t1"
## [98] "17\t1\t0.0\t1\t0 1"
## [99] "18\t1\t0.0\t1\t0 1"
## [100] "20\t2\t0.0\t2\t2"
## [101] "21\t1\t0.0\t2\t1"
## [102] "22\t3\t0.0\t2\t2 1"
## [103] "25\t1\t0.0\t2\t0 1"
## [104] "27\t4\t0.0\t2\t3 0 1"
## [105] "28\t2\t0.0\t2\t2"
## [106] "29\t1\t0.0\t2\t1"
## [107] "30\t2\t0.0\t3\t2"
## [108] "32\t2\t0.0\t3\t0 2"
## [109] "34\t1\t0.0\t3\t1"
## [110] "35\t3\t0.0\t3\t2 1"
## [111] "38\t1\t0.0\t3\t1"
## [112] "39\t3\t0.0\t3\t2 1"
## [113] "40\t1\t0.0\t4\t1"
## [114] "42\t3\t0.0\t4\t1 2"
## [115] "43\t1\t0.0\t4\t1"
## [116] "44\t3\t0.0\t4\t2 0 1"
## [117] "45\t1\t0.0\t4\t0 1"
## [118] "49\t1\t0.0\t4\t1"
## [119] "51\t3\t0.0\t4\t3"
## [120] "52\t5\t0.0\t4\t3 2"
## [121] "53\t2\t0.0\t4\t0 2"
## [122] "54\t1\t0.0\t4\t0 1"
## [123] "57\t1\t0.0\t4\t1"
## [124] "58\t6\t0.0\t4\t6"
## [125] "59\t3\t0.0\t4\t1 2"
## [126] "60\t2\t0.0\t4\t2"
## [127] "61\t1\t0.0\t4\t1"
## [128] "62\t2\t0.0\t4\t1 1"
## [129] "63\t1\t0.0\t4\t1"
## [130] "64\t2\t0.0\t4\t2"
## [131] "65\t1\t0.0\t4\t1"
## [132] "66\t1\t0.0\t4\t1"
## [133] "69\t1\t0.0\t4\t1"
## [134] "72\t2\t0.0\t4\t1 1"
## [135] "73\t3\t0.0\t4\t2 1"
## [136] "74\t2\t0.0\t4\t2"
## [137] "76\t3\t0.0\t4\t3"
## [138] "77\t4\t0.0\t4\t4"
## [139] "79\t3\t0.0\t4\t3"
## [140] "82\t1\t0.0\t4\t1"
## [141] "84\t1\t0.0\t4\t1"
## [142] "85\t1\t0.0\t4\t1"
## [143] "86\t5\t0.0\t4\t4 1"
## [144] "87\t1\t0.0\t4\t1"
## [145] "89\t4\t0.0\t4\t3 1"
## [146] "92\t1\t0.0\t4\t1"
## [147] "93\t2\t0.0\t4\t1 1"
## [148] "94\t3\t0.0\t4\t3"
## [149] "95\t1\t0.0\t4\t1"
## [150] "96\t2\t0.0\t4\t2"
## [151] "97\t2\t0.0\t4\t1 1"
## [152] "101\t3\t0.0\t4\t2 1"
## [153] "102\t3\t0.0\t4\t3"
## [154] "105\t1\t0.0\t4\t1"
## [155] "106\t2\t0.0\t4\t2"
## [156] "107\t1\t0.0\t4\t1"
## [157] "110\t1\t0.0\t4\t0 0 1"
## [158] "111\t1\t0.0\t4\t1"
## [159] "112\t1\t0.0\t4\t1"
## [160] "115\t1\t0.0\t4\t1"
## [161] "116\t2\t0.0\t4\t2"
## [162] "118\t4\t0.0\t4\t4"
## [163] "120\t1\t0.0\t4\t1"
## [164] "122\t2\t0.0\t4\t2"
## [165] "125\t1\t0.0\t4\t1"
## [166] "127\t1\t0.0\t4\t1"
## [167] "131\t1\t0.0\t4\t1"
## [168] "134\t1\t0.0\t4\t1"
## [169] "135\t1\t0.0\t4\t1"
## [170] "136\t1\t0.0\t4\t1"
## [171] "140\t1\t0.0\t4\t0 1"
## [172] "145\t1\t0.0\t4\t0 1"
## [173] "146\t3\t0.0\t4\t3"
## [174] "147\t1\t0.0\t4\t0 1"
## [175] "165\t1\t0.0\t4\t1"
## [176] "170\t2\t0.0\t4\t2"
## [177] "186\t1\t0.0\t4\t1"
##
## [[57]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/71ARNA2_S57_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/71ARNA2_S57_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/71ARNA2_S57_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/71ARNA2_S57_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.20 s (114 us/read; 0.53 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 1,793"
## [9] " Read 1 with adapter: 7 (0.4%)"
## [10] " Read 2 with adapter: 33 (1.8%)"
## [11] "Pairs written (passing filters): 1,793 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 753,060 bp"
## [14] " Read 1: 351,428 bp"
## [15] " Read 2: 401,632 bp"
## [16] "Total written (filtered): 750,424 bp (99.6%)"
## [17] " Read 1: 350,991 bp"
## [18] " Read 2: 399,433 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 7 times"
## [27] ""
## [28] "No. of allowed errors:"
## [29] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [30] ""
## [31] "Bases preceding removed adapters:"
## [32] " A: 57.1%"
## [33] " C: 0.0%"
## [34] " G: 42.9%"
## [35] " T: 0.0%"
## [36] " none/other: 0.0%"
## [37] ""
## [38] "Overview of removed sequences"
## [39] "length\tcount\texpect\tmax.err\terror counts"
## [40] "16\t1\t0.0\t1\t1"
## [41] "63\t3\t0.0\t2\t3"
## [42] "74\t2\t0.0\t2\t2"
## [43] "84\t1\t0.0\t2\t1"
## [44] ""
## [45] ""
## [46] "=== Second read: Adapter 3 ==="
## [47] ""
## [48] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [49] ""
## [50] "=== Second read: Adapter 4 ==="
## [51] ""
## [52] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 33 times"
## [53] ""
## [54] "No. of allowed errors:"
## [55] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [56] ""
## [57] "Bases preceding removed adapters:"
## [58] " A: 75.8%"
## [59] " C: 21.2%"
## [60] " G: 0.0%"
## [61] " T: 3.0%"
## [62] " none/other: 0.0%"
## [63] ""
## [64] "Overview of removed sequences"
## [65] "length\tcount\texpect\tmax.err\terror counts"
## [66] "9\t1\t0.0\t0\t1"
## [67] "12\t1\t0.0\t1\t0 1"
## [68] "13\t1\t0.0\t1\t0 1"
## [69] "14\t1\t0.0\t1\t0 1"
## [70] "18\t1\t0.0\t1\t1"
## [71] "26\t1\t0.0\t2\t0 0 1"
## [72] "29\t1\t0.0\t2\t1"
## [73] "39\t2\t0.0\t3\t2"
## [74] "43\t1\t0.0\t4\t1"
## [75] "44\t1\t0.0\t4\t1"
## [76] "46\t1\t0.0\t4\t1"
## [77] "49\t1\t0.0\t4\t1"
## [78] "52\t2\t0.0\t4\t2"
## [79] "54\t1\t0.0\t4\t1"
## [80] "59\t1\t0.0\t4\t1"
## [81] "63\t1\t0.0\t4\t1"
## [82] "67\t1\t0.0\t4\t1"
## [83] "79\t2\t0.0\t4\t2"
## [84] "91\t3\t0.0\t4\t2 0 1"
## [85] "92\t1\t0.0\t4\t1"
## [86] "98\t1\t0.0\t4\t1"
## [87] "102\t2\t0.0\t4\t2"
## [88] "112\t1\t0.0\t4\t1"
## [89] "115\t1\t0.0\t4\t1"
## [90] "116\t1\t0.0\t4\t1"
## [91] "138\t1\t0.0\t4\t1"
## [92] "165\t1\t0.0\t4\t1"
##
## [[58]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/71ARNA3_S58_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/71ARNA3_S58_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/71ARNA3_S58_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/71ARNA3_S58_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.04 s (171 us/read; 0.35 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 209"
## [9] " Read 1 with adapter: 2 (1.0%)"
## [10] " Read 2 with adapter: 9 (4.3%)"
## [11] "Pairs written (passing filters): 208 (99.5%)"
## [12] ""
## [13] "Total basepairs processed: 87,780 bp"
## [14] " Read 1: 40,964 bp"
## [15] " Read 2: 46,816 bp"
## [16] "Total written (filtered): 86,475 bp (98.5%)"
## [17] " Read 1: 40,628 bp"
## [18] " Read 2: 45,847 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 2 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "36\t1\t0.0\t3\t0 0 0 1"
## [30] "73\t1\t0.0\t4\t0 0 0 0 1"
## [31] ""
## [32] ""
## [33] "=== First read: Adapter 2 ==="
## [34] ""
## [35] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 1 times"
## [36] ""
## [37] "No. of allowed errors:"
## [38] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [39] ""
## [40] "Bases preceding removed adapters:"
## [41] " A: 100.0%"
## [42] " C: 0.0%"
## [43] " G: 0.0%"
## [44] " T: 0.0%"
## [45] " none/other: 0.0%"
## [46] ""
## [47] "Overview of removed sequences"
## [48] "length\tcount\texpect\tmax.err\terror counts"
## [49] "140\t1\t0.0\t2\t1"
## [50] ""
## [51] ""
## [52] "=== Second read: Adapter 3 ==="
## [53] ""
## [54] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [55] ""
## [56] "=== Second read: Adapter 4 ==="
## [57] ""
## [58] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 10 times"
## [59] ""
## [60] "No. of allowed errors:"
## [61] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [62] ""
## [63] "Bases preceding removed adapters:"
## [64] " A: 70.0%"
## [65] " C: 0.0%"
## [66] " G: 0.0%"
## [67] " T: 30.0%"
## [68] " none/other: 0.0%"
## [69] ""
## [70] "Overview of removed sequences"
## [71] "length\tcount\texpect\tmax.err\terror counts"
## [72] "59\t1\t0.0\t4\t1"
## [73] "60\t1\t0.0\t4\t1"
## [74] "72\t1\t0.0\t4\t0 0 0 0 1"
## [75] "73\t1\t0.0\t4\t1"
## [76] "80\t1\t0.0\t4\t1"
## [77] "85\t1\t0.0\t4\t1"
## [78] "121\t1\t0.0\t4\t1"
## [79] "131\t1\t0.0\t4\t1"
## [80] "136\t1\t0.0\t4\t1"
## [81] "138\t1\t0.0\t4\t0 0 1"
##
## [[59]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/71B1_S59_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/71B1_S59_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/71B1_S59_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/71B1_S59_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.82 s (110 us/read; 0.55 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 16,557"
## [9] " Read 1 with adapter: 1 (0.0%)"
## [10] " Read 2 with adapter: 98 (0.6%)"
## [11] "Pairs written (passing filters): 16,557 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 6,953,940 bp"
## [14] " Read 1: 3,245,172 bp"
## [15] " Read 2: 3,708,768 bp"
## [16] "Total written (filtered): 6,948,082 bp (99.9%)"
## [17] " Read 1: 3,245,167 bp"
## [18] " Read 2: 3,702,915 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 1 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t16.2\t0\t1"
## [30] ""
## [31] ""
## [32] "=== First read: Adapter 2 ==="
## [33] ""
## [34] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 0 times"
## [35] ""
## [36] "=== Second read: Adapter 3 ==="
## [37] ""
## [38] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [39] ""
## [40] "=== Second read: Adapter 4 ==="
## [41] ""
## [42] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 99 times"
## [43] ""
## [44] "No. of allowed errors:"
## [45] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [46] ""
## [47] "Bases preceding removed adapters:"
## [48] " A: 57.6%"
## [49] " C: 40.4%"
## [50] " G: 1.0%"
## [51] " T: 1.0%"
## [52] " none/other: 0.0%"
## [53] ""
## [54] "Overview of removed sequences"
## [55] "length\tcount\texpect\tmax.err\terror counts"
## [56] "5\t3\t16.2\t0\t3"
## [57] "7\t2\t1.0\t0\t2"
## [58] "10\t1\t0.0\t1\t1"
## [59] "11\t1\t0.0\t1\t1"
## [60] "12\t1\t0.0\t1\t1"
## [61] "13\t1\t0.0\t1\t1"
## [62] "15\t2\t0.0\t1\t2"
## [63] "16\t2\t0.0\t1\t2"
## [64] "20\t1\t0.0\t2\t1"
## [65] "22\t2\t0.0\t2\t2"
## [66] "26\t1\t0.0\t2\t0 1"
## [67] "27\t3\t0.0\t2\t3"
## [68] "28\t1\t0.0\t2\t1"
## [69] "29\t1\t0.0\t2\t1"
## [70] "30\t1\t0.0\t3\t1"
## [71] "31\t1\t0.0\t3\t1"
## [72] "32\t3\t0.0\t3\t3"
## [73] "33\t2\t0.0\t3\t2"
## [74] "34\t4\t0.0\t3\t4"
## [75] "35\t1\t0.0\t3\t0 0 0 1"
## [76] "38\t1\t0.0\t3\t1"
## [77] "39\t4\t0.0\t3\t4"
## [78] "40\t2\t0.0\t4\t2"
## [79] "43\t2\t0.0\t4\t2"
## [80] "45\t1\t0.0\t4\t1"
## [81] "46\t2\t0.0\t4\t2"
## [82] "47\t2\t0.0\t4\t2"
## [83] "48\t1\t0.0\t4\t1"
## [84] "52\t1\t0.0\t4\t1"
## [85] "59\t2\t0.0\t4\t1 1"
## [86] "61\t1\t0.0\t4\t1"
## [87] "63\t1\t0.0\t4\t1"
## [88] "64\t1\t0.0\t4\t1"
## [89] "66\t3\t0.0\t4\t3"
## [90] "67\t1\t0.0\t4\t1"
## [91] "72\t3\t0.0\t4\t2 1"
## [92] "73\t1\t0.0\t4\t1"
## [93] "74\t1\t0.0\t4\t1"
## [94] "75\t1\t0.0\t4\t1"
## [95] "79\t1\t0.0\t4\t1"
## [96] "82\t3\t0.0\t4\t3"
## [97] "83\t2\t0.0\t4\t2"
## [98] "84\t3\t0.0\t4\t2 1"
## [99] "85\t1\t0.0\t4\t1"
## [100] "86\t1\t0.0\t4\t1"
## [101] "87\t3\t0.0\t4\t3"
## [102] "88\t1\t0.0\t4\t1"
## [103] "93\t3\t0.0\t4\t3"
## [104] "96\t1\t0.0\t4\t1"
## [105] "99\t2\t0.0\t4\t2"
## [106] "103\t2\t0.0\t4\t2"
## [107] "109\t1\t0.0\t4\t1"
## [108] "111\t2\t0.0\t4\t1 1"
## [109] "112\t2\t0.0\t4\t1 1"
## [110] "122\t1\t0.0\t4\t1"
## [111] "126\t1\t0.0\t4\t1"
## [112] "127\t1\t0.0\t4\t1"
## [113] "136\t1\t0.0\t4\t1"
## [114] "142\t1\t0.0\t4\t1"
## [115] "144\t1\t0.0\t4\t0 1"
##
## [[60]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/71BRNA4_S60_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/71BRNA4_S60_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/71BRNA4_S60_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/71BRNA4_S60_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.14 s (125 us/read; 0.48 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 1,149"
## [9] " Read 1 with adapter: 30 (2.6%)"
## [10] " Read 2 with adapter: 46 (4.0%)"
## [11] "Pairs written (passing filters): 1,148 (99.9%)"
## [12] ""
## [13] "Total basepairs processed: 482,580 bp"
## [14] " Read 1: 225,204 bp"
## [15] " Read 2: 257,376 bp"
## [16] "Total written (filtered): 476,004 bp (98.6%)"
## [17] " Read 1: 223,017 bp"
## [18] " Read 2: 252,987 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 1 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "45\t1\t0.0\t4\t0 1"
## [30] ""
## [31] ""
## [32] "=== First read: Adapter 2 ==="
## [33] ""
## [34] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 29 times"
## [35] ""
## [36] "No. of allowed errors:"
## [37] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [38] ""
## [39] "Bases preceding removed adapters:"
## [40] " A: 34.5%"
## [41] " C: 13.8%"
## [42] " G: 51.7%"
## [43] " T: 0.0%"
## [44] " none/other: 0.0%"
## [45] ""
## [46] "Overview of removed sequences"
## [47] "length\tcount\texpect\tmax.err\terror counts"
## [48] "8\t1\t0.0\t0\t1"
## [49] "14\t1\t0.0\t1\t1"
## [50] "21\t1\t0.0\t2\t1"
## [51] "23\t2\t0.0\t2\t2"
## [52] "52\t4\t0.0\t2\t3 1"
## [53] "61\t4\t0.0\t2\t4"
## [54] "62\t1\t0.0\t2\t1"
## [55] "75\t2\t0.0\t2\t2"
## [56] "82\t5\t0.0\t2\t5"
## [57] "90\t1\t0.0\t2\t1"
## [58] "91\t4\t0.0\t2\t4"
## [59] "93\t1\t0.0\t2\t1"
## [60] "118\t2\t0.0\t2\t2"
## [61] ""
## [62] ""
## [63] "=== Second read: Adapter 3 ==="
## [64] ""
## [65] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [66] ""
## [67] "=== Second read: Adapter 4 ==="
## [68] ""
## [69] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 46 times"
## [70] ""
## [71] "No. of allowed errors:"
## [72] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [73] ""
## [74] "Bases preceding removed adapters:"
## [75] " A: 84.8%"
## [76] " C: 10.9%"
## [77] " G: 4.3%"
## [78] " T: 0.0%"
## [79] " none/other: 0.0%"
## [80] "WARNING:"
## [81] " The adapter is preceded by \"A\" extremely often."
## [82] " The provided adapter sequence could be incomplete at its 3' end."
## [83] ""
## [84] "Overview of removed sequences"
## [85] "length\tcount\texpect\tmax.err\terror counts"
## [86] "5\t1\t1.1\t0\t1"
## [87] "35\t1\t0.0\t3\t1"
## [88] "36\t1\t0.0\t3\t0 0 1"
## [89] "41\t1\t0.0\t4\t1"
## [90] "42\t1\t0.0\t4\t1"
## [91] "48\t1\t0.0\t4\t0 0 1"
## [92] "49\t1\t0.0\t4\t1"
## [93] "51\t2\t0.0\t4\t0 2"
## [94] "66\t1\t0.0\t4\t1"
## [95] "74\t1\t0.0\t4\t0 1"
## [96] "80\t4\t0.0\t4\t4"
## [97] "83\t1\t0.0\t4\t1"
## [98] "89\t4\t0.0\t4\t0 4"
## [99] "90\t1\t0.0\t4\t1"
## [100] "94\t1\t0.0\t4\t1"
## [101] "103\t2\t0.0\t4\t2"
## [102] "107\t1\t0.0\t4\t1"
## [103] "109\t1\t0.0\t4\t1"
## [104] "110\t5\t0.0\t4\t3 2"
## [105] "112\t1\t0.0\t4\t0 1"
## [106] "117\t1\t0.0\t4\t0 1"
## [107] "118\t1\t0.0\t4\t1"
## [108] "119\t5\t0.0\t4\t5"
## [109] "121\t1\t0.0\t4\t1"
## [110] "128\t1\t0.0\t4\t1"
## [111] "133\t1\t0.0\t4\t1"
## [112] "136\t1\t0.0\t4\t0 1"
## [113] "146\t2\t0.0\t4\t2"
## [114] "183\t1\t0.0\t4\t1"
## [115] ""
## [116] ""
## [117] "WARNING:"
## [118] " One or more of your adapter sequences may be incomplete."
## [119] " Please see the detailed output above."
##
## [[61]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/BA11_S61_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/BA11_S61_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/BA11_S61_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/BA11_S61_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.04 s (138 us/read; 0.44 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 281"
## [9] " Read 1 with adapter: 0 (0.0%)"
## [10] " Read 2 with adapter: 5 (1.8%)"
## [11] "Pairs written (passing filters): 281 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 118,020 bp"
## [14] " Read 1: 55,076 bp"
## [15] " Read 2: 62,944 bp"
## [16] "Total written (filtered): 117,669 bp (99.7%)"
## [17] " Read 1: 55,076 bp"
## [18] " Read 2: 62,593 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 0 times"
## [27] ""
## [28] "=== Second read: Adapter 3 ==="
## [29] ""
## [30] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [31] ""
## [32] "=== Second read: Adapter 4 ==="
## [33] ""
## [34] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 5 times"
## [35] ""
## [36] "No. of allowed errors:"
## [37] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [38] ""
## [39] "Bases preceding removed adapters:"
## [40] " A: 80.0%"
## [41] " C: 0.0%"
## [42] " G: 20.0%"
## [43] " T: 0.0%"
## [44] " none/other: 0.0%"
## [45] ""
## [46] "Overview of removed sequences"
## [47] "length\tcount\texpect\tmax.err\terror counts"
## [48] "30\t1\t0.0\t3\t1"
## [49] "53\t1\t0.0\t4\t1"
## [50] "76\t1\t0.0\t4\t1"
## [51] "94\t1\t0.0\t4\t1"
## [52] "98\t1\t0.0\t4\t1"
##
## [[62]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/BA12_S62_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/BA12_S62_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/BA12_S62_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/BA12_S62_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.09 s (119 us/read; 0.51 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 793"
## [9] " Read 1 with adapter: 4 (0.5%)"
## [10] " Read 2 with adapter: 12 (1.5%)"
## [11] "Pairs written (passing filters): 793 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 333,060 bp"
## [14] " Read 1: 155,428 bp"
## [15] " Read 2: 177,632 bp"
## [16] "Total written (filtered): 331,359 bp (99.5%)"
## [17] " Read 1: 154,886 bp"
## [18] " Read 2: 176,473 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 4 times"
## [27] ""
## [28] "No. of allowed errors:"
## [29] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [30] ""
## [31] "Bases preceding removed adapters:"
## [32] " A: 0.0%"
## [33] " C: 0.0%"
## [34] " G: 100.0%"
## [35] " T: 0.0%"
## [36] " none/other: 0.0%"
## [37] ""
## [38] "Overview of removed sequences"
## [39] "length\tcount\texpect\tmax.err\terror counts"
## [40] "104\t1\t0.0\t2\t1"
## [41] "146\t3\t0.0\t2\t3"
## [42] ""
## [43] ""
## [44] "=== Second read: Adapter 3 ==="
## [45] ""
## [46] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [47] ""
## [48] "=== Second read: Adapter 4 ==="
## [49] ""
## [50] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 12 times"
## [51] ""
## [52] "No. of allowed errors:"
## [53] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [54] ""
## [55] "Bases preceding removed adapters:"
## [56] " A: 50.0%"
## [57] " C: 0.0%"
## [58] " G: 41.7%"
## [59] " T: 8.3%"
## [60] " none/other: 0.0%"
## [61] ""
## [62] "Overview of removed sequences"
## [63] "length\tcount\texpect\tmax.err\terror counts"
## [64] "7\t1\t0.0\t0\t1"
## [65] "8\t1\t0.0\t0\t1"
## [66] "51\t1\t0.0\t4\t1"
## [67] "56\t1\t0.0\t4\t1"
## [68] "67\t1\t0.0\t4\t0 1"
## [69] "72\t1\t0.0\t4\t1"
## [70] "106\t1\t0.0\t4\t1"
## [71] "132\t1\t0.0\t4\t1"
## [72] "138\t1\t0.0\t4\t1"
## [73] "174\t3\t0.0\t4\t2 1"
##
## [[63]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/BA13_S63_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/BA13_S63_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/BA13_S63_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/BA13_S63_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.21 s (112 us/read; 0.53 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 1,909"
## [9] " Read 1 with adapter: 0 (0.0%)"
## [10] " Read 2 with adapter: 12 (0.6%)"
## [11] "Pairs written (passing filters): 1,908 (99.9%)"
## [12] ""
## [13] "Total basepairs processed: 801,780 bp"
## [14] " Read 1: 374,164 bp"
## [15] " Read 2: 427,616 bp"
## [16] "Total written (filtered): 800,835 bp (99.9%)"
## [17] " Read 1: 373,968 bp"
## [18] " Read 2: 426,867 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 0 times"
## [27] ""
## [28] "=== Second read: Adapter 3 ==="
## [29] ""
## [30] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [31] ""
## [32] "=== Second read: Adapter 4 ==="
## [33] ""
## [34] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 12 times"
## [35] ""
## [36] "No. of allowed errors:"
## [37] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [38] ""
## [39] "Bases preceding removed adapters:"
## [40] " A: 75.0%"
## [41] " C: 16.7%"
## [42] " G: 8.3%"
## [43] " T: 0.0%"
## [44] " none/other: 0.0%"
## [45] ""
## [46] "Overview of removed sequences"
## [47] "length\tcount\texpect\tmax.err\terror counts"
## [48] "5\t2\t1.9\t0\t2"
## [49] "14\t1\t0.0\t1\t1"
## [50] "16\t1\t0.0\t1\t1"
## [51] "42\t1\t0.0\t4\t0 1"
## [52] "57\t2\t0.0\t4\t1 1"
## [53] "68\t1\t0.0\t4\t1"
## [54] "73\t1\t0.0\t4\t0 1"
## [55] "82\t1\t0.0\t4\t1"
## [56] "106\t1\t0.0\t4\t1"
## [57] "179\t1\t0.0\t4\t1"
##
## [[64]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/BA1DF1_S66_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/BA1DF1_S66_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/BA1DF1_S66_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/BA1DF1_S66_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 2.49 s (102 us/read; 0.59 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 24,379"
## [9] " Read 1 with adapter: 5 (0.0%)"
## [10] " Read 2 with adapter: 428 (1.8%)"
## [11] "Pairs written (passing filters): 24,379 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 10,239,180 bp"
## [14] " Read 1: 4,778,284 bp"
## [15] " Read 2: 5,460,896 bp"
## [16] "Total written (filtered): 10,209,110 bp (99.7%)"
## [17] " Read 1: 4,778,181 bp"
## [18] " Read 2: 5,430,929 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 4 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t23.8\t0\t1"
## [30] "8\t1\t0.4\t0\t1"
## [31] "22\t1\t0.0\t2\t1"
## [32] "30\t1\t0.0\t3\t1"
## [33] ""
## [34] ""
## [35] "=== First read: Adapter 2 ==="
## [36] ""
## [37] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 1 times"
## [38] ""
## [39] "No. of allowed errors:"
## [40] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [41] ""
## [42] "Bases preceding removed adapters:"
## [43] " A: 0.0%"
## [44] " C: 0.0%"
## [45] " G: 100.0%"
## [46] " T: 0.0%"
## [47] " none/other: 0.0%"
## [48] ""
## [49] "Overview of removed sequences"
## [50] "length\tcount\texpect\tmax.err\terror counts"
## [51] "38\t1\t0.0\t2\t1"
## [52] ""
## [53] ""
## [54] "=== Second read: Adapter 3 ==="
## [55] ""
## [56] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 2 times"
## [57] ""
## [58] "No. of allowed errors:"
## [59] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [60] ""
## [61] "Overview of removed sequences"
## [62] "length\tcount\texpect\tmax.err\terror counts"
## [63] "7\t1\t1.5\t0\t1"
## [64] "9\t1\t0.1\t0\t1"
## [65] ""
## [66] ""
## [67] "=== Second read: Adapter 4 ==="
## [68] ""
## [69] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 426 times"
## [70] ""
## [71] "No. of allowed errors:"
## [72] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [73] ""
## [74] "Bases preceding removed adapters:"
## [75] " A: 91.5%"
## [76] " C: 7.3%"
## [77] " G: 0.9%"
## [78] " T: 0.2%"
## [79] " none/other: 0.0%"
## [80] "WARNING:"
## [81] " The adapter is preceded by \"A\" extremely often."
## [82] " The provided adapter sequence could be incomplete at its 3' end."
## [83] ""
## [84] "Overview of removed sequences"
## [85] "length\tcount\texpect\tmax.err\terror counts"
## [86] "5\t32\t23.8\t0\t32"
## [87] "6\t1\t6.0\t0\t1"
## [88] "7\t2\t1.5\t0\t2"
## [89] "8\t9\t0.4\t0\t9"
## [90] "9\t4\t0.1\t0\t4"
## [91] "10\t2\t0.0\t1\t2"
## [92] "12\t3\t0.0\t1\t3"
## [93] "13\t2\t0.0\t1\t2"
## [94] "14\t12\t0.0\t1\t12"
## [95] "15\t1\t0.0\t1\t1"
## [96] "16\t5\t0.0\t1\t5"
## [97] "17\t2\t0.0\t1\t2"
## [98] "18\t3\t0.0\t1\t2 1"
## [99] "19\t3\t0.0\t1\t2 1"
## [100] "20\t3\t0.0\t2\t2 1"
## [101] "21\t3\t0.0\t2\t1 2"
## [102] "22\t2\t0.0\t2\t2"
## [103] "23\t4\t0.0\t2\t2 2"
## [104] "24\t2\t0.0\t2\t1 1"
## [105] "25\t2\t0.0\t2\t1 1"
## [106] "26\t2\t0.0\t2\t2"
## [107] "27\t3\t0.0\t2\t1 2"
## [108] "29\t1\t0.0\t2\t1"
## [109] "30\t2\t0.0\t3\t1 0 0 1"
## [110] "31\t1\t0.0\t3\t0 0 1"
## [111] "32\t1\t0.0\t3\t0 1"
## [112] "33\t3\t0.0\t3\t3"
## [113] "34\t1\t0.0\t3\t1"
## [114] "35\t3\t0.0\t3\t1 2"
## [115] "36\t2\t0.0\t3\t1 1"
## [116] "38\t1\t0.0\t3\t1"
## [117] "41\t3\t0.0\t4\t3"
## [118] "42\t2\t0.0\t4\t2"
## [119] "44\t1\t0.0\t4\t1"
## [120] "45\t2\t0.0\t4\t2"
## [121] "46\t11\t0.0\t4\t7 2 2"
## [122] "47\t6\t0.0\t4\t6"
## [123] "48\t3\t0.0\t4\t1 1 0 1"
## [124] "51\t2\t0.0\t4\t2"
## [125] "52\t9\t0.0\t4\t8 0 1"
## [126] "53\t3\t0.0\t4\t0 1 1 1"
## [127] "54\t4\t0.0\t4\t4"
## [128] "55\t4\t0.0\t4\t3 1"
## [129] "56\t1\t0.0\t4\t1"
## [130] "57\t3\t0.0\t4\t3"
## [131] "58\t2\t0.0\t4\t2"
## [132] "60\t1\t0.0\t4\t1"
## [133] "61\t1\t0.0\t4\t1"
## [134] "62\t1\t0.0\t4\t1"
## [135] "63\t3\t0.0\t4\t3"
## [136] "64\t3\t0.0\t4\t3"
## [137] "65\t3\t0.0\t4\t2 1"
## [138] "66\t4\t0.0\t4\t3 1"
## [139] "67\t2\t0.0\t4\t2"
## [140] "70\t1\t0.0\t4\t1"
## [141] "71\t2\t0.0\t4\t2"
## [142] "72\t2\t0.0\t4\t2"
## [143] "74\t4\t0.0\t4\t4"
## [144] "75\t4\t0.0\t4\t3 1"
## [145] "76\t2\t0.0\t4\t2"
## [146] "77\t3\t0.0\t4\t3"
## [147] "79\t2\t0.0\t4\t2"
## [148] "80\t1\t0.0\t4\t1"
## [149] "82\t2\t0.0\t4\t1 1"
## [150] "83\t1\t0.0\t4\t1"
## [151] "84\t2\t0.0\t4\t2"
## [152] "85\t4\t0.0\t4\t3 1"
## [153] "86\t6\t0.0\t4\t6"
## [154] "87\t1\t0.0\t4\t1"
## [155] "88\t5\t0.0\t4\t5"
## [156] "89\t1\t0.0\t4\t1"
## [157] "91\t2\t0.0\t4\t2"
## [158] "92\t1\t0.0\t4\t1"
## [159] "93\t1\t0.0\t4\t1"
## [160] "94\t5\t0.0\t4\t3 2"
## [161] "95\t2\t0.0\t4\t2"
## [162] "96\t1\t0.0\t4\t1"
## [163] "97\t4\t0.0\t4\t4"
## [164] "98\t2\t0.0\t4\t1 1"
## [165] "99\t4\t0.0\t4\t4"
## [166] "100\t2\t0.0\t4\t1 1"
## [167] "102\t4\t0.0\t4\t4"
## [168] "104\t18\t0.0\t4\t16 2"
## [169] "105\t96\t0.0\t4\t86 10"
## [170] "106\t7\t0.0\t4\t7"
## [171] "107\t1\t0.0\t4\t1"
## [172] "108\t3\t0.0\t4\t2 1"
## [173] "110\t4\t0.0\t4\t2 2"
## [174] "112\t2\t0.0\t4\t2"
## [175] "113\t1\t0.0\t4\t1"
## [176] "114\t1\t0.0\t4\t1"
## [177] "115\t4\t0.0\t4\t3 0 0 0 1"
## [178] "116\t2\t0.0\t4\t2"
## [179] "118\t1\t0.0\t4\t1"
## [180] "119\t3\t0.0\t4\t3"
## [181] "121\t2\t0.0\t4\t2"
## [182] "123\t1\t0.0\t4\t1"
## [183] "124\t1\t0.0\t4\t1"
## [184] "127\t3\t0.0\t4\t3"
## [185] "128\t1\t0.0\t4\t1"
## [186] "131\t2\t0.0\t4\t2"
## [187] "132\t1\t0.0\t4\t1"
## [188] "135\t1\t0.0\t4\t1"
## [189] "146\t2\t0.0\t4\t2"
## [190] "147\t3\t0.0\t4\t3"
## [191] "149\t1\t0.0\t4\t1"
## [192] "153\t1\t0.0\t4\t1"
## [193] "164\t1\t0.0\t4\t1"
## [194] "165\t1\t0.0\t4\t1"
## [195] ""
## [196] ""
## [197] "WARNING:"
## [198] " One or more of your adapter sequences may be incomplete."
## [199] " Please see the detailed output above."
##
## [[65]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/BA1DF2_S67_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/BA1DF2_S67_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/BA1DF2_S67_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/BA1DF2_S67_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.14 s (103 us/read; 0.58 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 11,111"
## [9] " Read 1 with adapter: 3 (0.0%)"
## [10] " Read 2 with adapter: 129 (1.2%)"
## [11] "Pairs written (passing filters): 11,111 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 4,666,620 bp"
## [14] " Read 1: 2,177,756 bp"
## [15] " Read 2: 2,488,864 bp"
## [16] "Total written (filtered): 4,658,068 bp (99.8%)"
## [17] " Read 1: 2,177,659 bp"
## [18] " Read 2: 2,480,409 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 2 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t10.9\t0\t1"
## [30] "33\t1\t0.0\t3\t1"
## [31] ""
## [32] ""
## [33] "=== First read: Adapter 2 ==="
## [34] ""
## [35] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 1 times"
## [36] ""
## [37] "No. of allowed errors:"
## [38] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [39] ""
## [40] "Bases preceding removed adapters:"
## [41] " A: 100.0%"
## [42] " C: 0.0%"
## [43] " G: 0.0%"
## [44] " T: 0.0%"
## [45] " none/other: 0.0%"
## [46] ""
## [47] "Overview of removed sequences"
## [48] "length\tcount\texpect\tmax.err\terror counts"
## [49] "59\t1\t0.0\t2\t1"
## [50] ""
## [51] ""
## [52] "=== Second read: Adapter 3 ==="
## [53] ""
## [54] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 1 times"
## [55] ""
## [56] "No. of allowed errors:"
## [57] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [58] ""
## [59] "Overview of removed sequences"
## [60] "length\tcount\texpect\tmax.err\terror counts"
## [61] "8\t1\t0.2\t0\t1"
## [62] ""
## [63] ""
## [64] "=== Second read: Adapter 4 ==="
## [65] ""
## [66] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 128 times"
## [67] ""
## [68] "No. of allowed errors:"
## [69] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [70] ""
## [71] "Bases preceding removed adapters:"
## [72] " A: 93.0%"
## [73] " C: 7.0%"
## [74] " G: 0.0%"
## [75] " T: 0.0%"
## [76] " none/other: 0.0%"
## [77] "WARNING:"
## [78] " The adapter is preceded by \"A\" extremely often."
## [79] " The provided adapter sequence could be incomplete at its 3' end."
## [80] ""
## [81] "Overview of removed sequences"
## [82] "length\tcount\texpect\tmax.err\terror counts"
## [83] "5\t9\t10.9\t0\t9"
## [84] "9\t1\t0.0\t0\t1"
## [85] "11\t1\t0.0\t1\t1"
## [86] "12\t1\t0.0\t1\t1"
## [87] "14\t4\t0.0\t1\t2 2"
## [88] "15\t2\t0.0\t1\t2"
## [89] "17\t2\t0.0\t1\t2"
## [90] "18\t1\t0.0\t1\t1"
## [91] "20\t1\t0.0\t2\t1"
## [92] "21\t2\t0.0\t2\t1 0 1"
## [93] "22\t2\t0.0\t2\t1 0 1"
## [94] "24\t1\t0.0\t2\t0 1"
## [95] "26\t1\t0.0\t2\t1"
## [96] "27\t3\t0.0\t2\t2 0 1"
## [97] "28\t1\t0.0\t2\t1"
## [98] "29\t1\t0.0\t2\t1"
## [99] "30\t1\t0.0\t3\t1"
## [100] "31\t2\t0.0\t3\t1 1"
## [101] "33\t1\t0.0\t3\t1"
## [102] "34\t1\t0.0\t3\t1"
## [103] "35\t1\t0.0\t3\t0 1"
## [104] "38\t1\t0.0\t3\t1"
## [105] "39\t1\t0.0\t3\t1"
## [106] "40\t3\t0.0\t4\t1 2"
## [107] "43\t1\t0.0\t4\t1"
## [108] "45\t1\t0.0\t4\t1"
## [109] "46\t1\t0.0\t4\t1"
## [110] "47\t1\t0.0\t4\t1"
## [111] "48\t1\t0.0\t4\t1"
## [112] "51\t2\t0.0\t4\t2"
## [113] "52\t5\t0.0\t4\t4 1"
## [114] "53\t1\t0.0\t4\t0 0 0 0 1"
## [115] "55\t1\t0.0\t4\t1"
## [116] "57\t2\t0.0\t4\t2"
## [117] "59\t1\t0.0\t4\t1"
## [118] "60\t1\t0.0\t4\t1"
## [119] "61\t1\t0.0\t4\t1"
## [120] "62\t1\t0.0\t4\t1"
## [121] "63\t1\t0.0\t4\t1"
## [122] "70\t1\t0.0\t4\t1"
## [123] "71\t1\t0.0\t4\t1"
## [124] "72\t3\t0.0\t4\t2 1"
## [125] "73\t2\t0.0\t4\t2"
## [126] "77\t1\t0.0\t4\t1"
## [127] "80\t1\t0.0\t4\t1"
## [128] "82\t1\t0.0\t4\t1"
## [129] "85\t3\t0.0\t4\t2 1"
## [130] "86\t1\t0.0\t4\t0 1"
## [131] "87\t2\t0.0\t4\t2"
## [132] "88\t1\t0.0\t4\t1"
## [133] "97\t1\t0.0\t4\t1"
## [134] "100\t1\t0.0\t4\t0 1"
## [135] "103\t1\t0.0\t4\t1"
## [136] "104\t4\t0.0\t4\t4"
## [137] "105\t26\t0.0\t4\t24 2"
## [138] "106\t2\t0.0\t4\t2"
## [139] "107\t1\t0.0\t4\t1"
## [140] "110\t1\t0.0\t4\t1"
## [141] "112\t1\t0.0\t4\t0 1"
## [142] "119\t1\t0.0\t4\t1"
## [143] "128\t1\t0.0\t4\t1"
## [144] "131\t1\t0.0\t4\t1"
## [145] "133\t1\t0.0\t4\t1"
## [146] "137\t1\t0.0\t4\t1"
## [147] "147\t1\t0.0\t4\t1"
## [148] "149\t1\t0.0\t4\t1"
## [149] "153\t1\t0.0\t4\t1"
## [150] ""
## [151] ""
## [152] "WARNING:"
## [153] " One or more of your adapter sequences may be incomplete."
## [154] " Please see the detailed output above."
##
## [[66]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/BA1DFRNA1_S64_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/BA1DFRNA1_S64_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/BA1DFRNA1_S64_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/BA1DFRNA1_S64_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 1.71 s (101 us/read; 0.60 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 17,045"
## [9] " Read 1 with adapter: 71 (0.4%)"
## [10] " Read 2 with adapter: 684 (4.0%)"
## [11] "Pairs written (passing filters): 17,044 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 7,158,900 bp"
## [14] " Read 1: 3,340,820 bp"
## [15] " Read 2: 3,818,080 bp"
## [16] "Total written (filtered): 7,104,091 bp (99.2%)"
## [17] " Read 1: 3,337,791 bp"
## [18] " Read 2: 3,766,300 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 1 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "66\t1\t0.0\t4\t0 0 1"
## [30] ""
## [31] ""
## [32] "=== First read: Adapter 2 ==="
## [33] ""
## [34] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 70 times"
## [35] ""
## [36] "No. of allowed errors:"
## [37] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [38] ""
## [39] "Bases preceding removed adapters:"
## [40] " A: 65.7%"
## [41] " C: 0.0%"
## [42] " G: 34.3%"
## [43] " T: 0.0%"
## [44] " none/other: 0.0%"
## [45] ""
## [46] "Overview of removed sequences"
## [47] "length\tcount\texpect\tmax.err\terror counts"
## [48] "5\t1\t16.6\t0\t1"
## [49] "6\t4\t4.2\t0\t4"
## [50] "7\t1\t1.0\t0\t1"
## [51] "8\t1\t0.3\t0\t1"
## [52] "9\t3\t0.1\t0\t3"
## [53] "10\t2\t0.0\t1\t1 1"
## [54] "11\t1\t0.0\t1\t1"
## [55] "16\t1\t0.0\t1\t1"
## [56] "18\t1\t0.0\t1\t1"
## [57] "19\t7\t0.0\t1\t7"
## [58] "20\t1\t0.0\t2\t1"
## [59] "22\t1\t0.0\t2\t1"
## [60] "23\t1\t0.0\t2\t1"
## [61] "27\t1\t0.0\t2\t1"
## [62] "28\t1\t0.0\t2\t1"
## [63] "30\t2\t0.0\t2\t2"
## [64] "32\t1\t0.0\t2\t1"
## [65] "33\t1\t0.0\t2\t1"
## [66] "36\t7\t0.0\t2\t7"
## [67] "38\t1\t0.0\t2\t1"
## [68] "39\t1\t0.0\t2\t1"
## [69] "41\t1\t0.0\t2\t1"
## [70] "42\t1\t0.0\t2\t0 1"
## [71] "43\t1\t0.0\t2\t1"
## [72] "44\t1\t0.0\t2\t1"
## [73] "45\t2\t0.0\t2\t2"
## [74] "46\t1\t0.0\t2\t1"
## [75] "48\t1\t0.0\t2\t1"
## [76] "49\t1\t0.0\t2\t1"
## [77] "60\t1\t0.0\t2\t1"
## [78] "64\t1\t0.0\t2\t1"
## [79] "68\t2\t0.0\t2\t2"
## [80] "69\t6\t0.0\t2\t6"
## [81] "70\t1\t0.0\t2\t1"
## [82] "71\t1\t0.0\t2\t1"
## [83] "75\t4\t0.0\t2\t4"
## [84] "83\t1\t0.0\t2\t1"
## [85] "84\t1\t0.0\t2\t1"
## [86] "109\t1\t0.0\t2\t1"
## [87] "130\t1\t0.0\t2\t1"
## [88] "150\t1\t0.0\t2\t1"
## [89] ""
## [90] ""
## [91] "=== Second read: Adapter 3 ==="
## [92] ""
## [93] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [94] ""
## [95] "=== Second read: Adapter 4 ==="
## [96] ""
## [97] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 684 times"
## [98] ""
## [99] "No. of allowed errors:"
## [100] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [101] ""
## [102] "Bases preceding removed adapters:"
## [103] " A: 97.5%"
## [104] " C: 2.0%"
## [105] " G: 0.1%"
## [106] " T: 0.3%"
## [107] " none/other: 0.0%"
## [108] "WARNING:"
## [109] " The adapter is preceded by \"A\" extremely often."
## [110] " The provided adapter sequence could be incomplete at its 3' end."
## [111] ""
## [112] "Overview of removed sequences"
## [113] "length\tcount\texpect\tmax.err\terror counts"
## [114] "5\t4\t16.6\t0\t4"
## [115] "6\t1\t4.2\t0\t1"
## [116] "7\t2\t1.0\t0\t2"
## [117] "8\t6\t0.3\t0\t6"
## [118] "9\t10\t0.1\t0\t10"
## [119] "10\t6\t0.0\t1\t6"
## [120] "11\t1\t0.0\t1\t1"
## [121] "12\t1\t0.0\t1\t1"
## [122] "13\t5\t0.0\t1\t3 2"
## [123] "14\t5\t0.0\t1\t4 1"
## [124] "15\t2\t0.0\t1\t1 1"
## [125] "16\t4\t0.0\t1\t3 1"
## [126] "17\t1\t0.0\t1\t1"
## [127] "18\t4\t0.0\t1\t4"
## [128] "20\t2\t0.0\t2\t1 1"
## [129] "21\t1\t0.0\t2\t0 1"
## [130] "22\t5\t0.0\t2\t4 1"
## [131] "23\t6\t0.0\t2\t4 2"
## [132] "24\t2\t0.0\t2\t2"
## [133] "25\t5\t0.0\t2\t4 0 1"
## [134] "26\t4\t0.0\t2\t1 2 1"
## [135] "27\t24\t0.0\t2\t20 2 2"
## [136] "28\t4\t0.0\t2\t3 0 1"
## [137] "29\t3\t0.0\t2\t1 1 1"
## [138] "30\t4\t0.0\t3\t3 0 1"
## [139] "31\t3\t0.0\t3\t3"
## [140] "32\t6\t0.0\t3\t6"
## [141] "33\t5\t0.0\t3\t3 1 1"
## [142] "34\t10\t0.0\t3\t7 2 1"
## [143] "35\t3\t0.0\t3\t3"
## [144] "36\t6\t0.0\t3\t5 1"
## [145] "37\t5\t0.0\t3\t3 2"
## [146] "38\t3\t0.0\t3\t1 1 1"
## [147] "39\t3\t0.0\t3\t2 1"
## [148] "40\t6\t0.0\t4\t6"
## [149] "41\t3\t0.0\t4\t3"
## [150] "42\t3\t0.0\t4\t0 2 0 1"
## [151] "43\t1\t0.0\t4\t1"
## [152] "44\t4\t0.0\t4\t2 0 1 1"
## [153] "45\t2\t0.0\t4\t2"
## [154] "46\t8\t0.0\t4\t6 2"
## [155] "47\t13\t0.0\t4\t8 4 0 1"
## [156] "48\t2\t0.0\t4\t2"
## [157] "50\t3\t0.0\t4\t2 0 0 1"
## [158] "51\t12\t0.0\t4\t11 1"
## [159] "52\t19\t0.0\t4\t15 4"
## [160] "53\t7\t0.0\t4\t6 1"
## [161] "54\t7\t0.0\t4\t4 2 0 1"
## [162] "55\t4\t0.0\t4\t4"
## [163] "56\t3\t0.0\t4\t2 0 1"
## [164] "57\t3\t0.0\t4\t2 1"
## [165] "58\t11\t0.0\t4\t9 0 1 1"
## [166] "60\t3\t0.0\t4\t3"
## [167] "61\t1\t0.0\t4\t1"
## [168] "62\t2\t0.0\t4\t2"
## [169] "64\t11\t0.0\t4\t8 2 1"
## [170] "65\t3\t0.0\t4\t3"
## [171] "66\t4\t0.0\t4\t3 1"
## [172] "67\t9\t0.0\t4\t8 1"
## [173] "69\t3\t0.0\t4\t2 0 1"
## [174] "70\t2\t0.0\t4\t2"
## [175] "71\t3\t0.0\t4\t2 0 1"
## [176] "72\t5\t0.0\t4\t4 1"
## [177] "73\t5\t0.0\t4\t3 1 1"
## [178] "74\t2\t0.0\t4\t2"
## [179] "75\t6\t0.0\t4\t6"
## [180] "76\t2\t0.0\t4\t2"
## [181] "77\t2\t0.0\t4\t2"
## [182] "78\t2\t0.0\t4\t2"
## [183] "79\t6\t0.0\t4\t6"
## [184] "80\t1\t0.0\t4\t1"
## [185] "81\t1\t0.0\t4\t1"
## [186] "83\t2\t0.0\t4\t1 0 1"
## [187] "84\t5\t0.0\t4\t5"
## [188] "85\t3\t0.0\t4\t2 0 1"
## [189] "86\t14\t0.0\t4\t13 1"
## [190] "87\t5\t0.0\t4\t5"
## [191] "88\t6\t0.0\t4\t6"
## [192] "89\t6\t0.0\t4\t6"
## [193] "90\t3\t0.0\t4\t3"
## [194] "91\t2\t0.0\t4\t2"
## [195] "92\t3\t0.0\t4\t3"
## [196] "94\t9\t0.0\t4\t8 1"
## [197] "95\t2\t0.0\t4\t2"
## [198] "96\t6\t0.0\t4\t5 1"
## [199] "97\t11\t0.0\t4\t9 2"
## [200] "98\t4\t0.0\t4\t3 1"
## [201] "99\t3\t0.0\t4\t3"
## [202] "100\t3\t0.0\t4\t3"
## [203] "101\t4\t0.0\t4\t4"
## [204] "103\t11\t0.0\t4\t10 1"
## [205] "104\t43\t0.0\t4\t41 1 0 1"
## [206] "105\t85\t0.0\t4\t76 8 1"
## [207] "106\t2\t0.0\t4\t2"
## [208] "108\t5\t0.0\t4\t5"
## [209] "109\t3\t0.0\t4\t3"
## [210] "110\t6\t0.0\t4\t6"
## [211] "111\t3\t0.0\t4\t3"
## [212] "112\t2\t0.0\t4\t2"
## [213] "113\t7\t0.0\t4\t7"
## [214] "114\t2\t0.0\t4\t2"
## [215] "115\t4\t0.0\t4\t4"
## [216] "116\t6\t0.0\t4\t6"
## [217] "117\t2\t0.0\t4\t2"
## [218] "118\t3\t0.0\t4\t3"
## [219] "119\t2\t0.0\t4\t2"
## [220] "120\t1\t0.0\t4\t1"
## [221] "121\t1\t0.0\t4\t1"
## [222] "122\t1\t0.0\t4\t1"
## [223] "123\t4\t0.0\t4\t4"
## [224] "124\t1\t0.0\t4\t1"
## [225] "125\t3\t0.0\t4\t2 1"
## [226] "126\t2\t0.0\t4\t2"
## [227] "127\t6\t0.0\t4\t6"
## [228] "128\t6\t0.0\t4\t6"
## [229] "129\t1\t0.0\t4\t1"
## [230] "130\t4\t0.0\t4\t3 1"
## [231] "131\t4\t0.0\t4\t4"
## [232] "132\t2\t0.0\t4\t2"
## [233] "133\t2\t0.0\t4\t2"
## [234] "135\t1\t0.0\t4\t1"
## [235] "136\t1\t0.0\t4\t1"
## [236] "137\t1\t0.0\t4\t1"
## [237] "139\t1\t0.0\t4\t1"
## [238] "140\t1\t0.0\t4\t1"
## [239] "141\t2\t0.0\t4\t2"
## [240] "142\t1\t0.0\t4\t1"
## [241] "144\t3\t0.0\t4\t3"
## [242] "145\t1\t0.0\t4\t1"
## [243] "146\t2\t0.0\t4\t2"
## [244] "149\t2\t0.0\t4\t2"
## [245] "151\t1\t0.0\t4\t1"
## [246] "153\t1\t0.0\t4\t1"
## [247] "154\t1\t0.0\t4\t1"
## [248] "158\t1\t0.0\t4\t1"
## [249] "161\t3\t0.0\t4\t3"
## [250] "162\t1\t0.0\t4\t1"
## [251] "165\t1\t0.0\t4\t1"
## [252] "167\t2\t0.0\t4\t2"
## [253] "171\t1\t0.0\t4\t1"
## [254] "178\t1\t0.0\t4\t1"
## [255] ""
## [256] ""
## [257] "WARNING:"
## [258] " One or more of your adapter sequences may be incomplete."
## [259] " Please see the detailed output above."
##
## [[67]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/BA1DFRNA2_S65_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/BA1DFRNA2_S65_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/BA1DFRNA2_S65_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/BA1DFRNA2_S65_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.92 s (101 us/read; 0.59 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 9,062"
## [9] " Read 1 with adapter: 89 (1.0%)"
## [10] " Read 2 with adapter: 348 (3.8%)"
## [11] "Pairs written (passing filters): 9,062 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 3,806,040 bp"
## [14] " Read 1: 1,776,152 bp"
## [15] " Read 2: 2,029,888 bp"
## [16] "Total written (filtered): 3,776,646 bp (99.2%)"
## [17] " Read 1: 1,771,398 bp"
## [18] " Read 2: 2,005,248 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 6 times"
## [23] ""
## [24] "No. of allowed errors:"
## [25] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [26] ""
## [27] "Overview of removed sequences"
## [28] "length\tcount\texpect\tmax.err\terror counts"
## [29] "5\t1\t8.8\t0\t1"
## [30] "6\t1\t2.2\t0\t1"
## [31] "7\t1\t0.6\t0\t1"
## [32] "10\t1\t0.0\t1\t1"
## [33] "16\t1\t0.0\t1\t1"
## [34] "32\t1\t0.0\t3\t1"
## [35] ""
## [36] ""
## [37] "=== First read: Adapter 2 ==="
## [38] ""
## [39] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 83 times"
## [40] ""
## [41] "No. of allowed errors:"
## [42] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [43] ""
## [44] "Bases preceding removed adapters:"
## [45] " A: 67.5%"
## [46] " C: 1.2%"
## [47] " G: 30.1%"
## [48] " T: 1.2%"
## [49] " none/other: 0.0%"
## [50] ""
## [51] "Overview of removed sequences"
## [52] "length\tcount\texpect\tmax.err\terror counts"
## [53] "6\t1\t2.2\t0\t1"
## [54] "7\t1\t0.6\t0\t1"
## [55] "8\t2\t0.1\t0\t2"
## [56] "10\t2\t0.0\t1\t2"
## [57] "15\t1\t0.0\t1\t1"
## [58] "16\t4\t0.0\t1\t4"
## [59] "18\t1\t0.0\t1\t1"
## [60] "19\t4\t0.0\t1\t4"
## [61] "20\t1\t0.0\t2\t1"
## [62] "25\t1\t0.0\t2\t1"
## [63] "27\t2\t0.0\t2\t2"
## [64] "31\t1\t0.0\t2\t1"
## [65] "32\t1\t0.0\t2\t1"
## [66] "33\t1\t0.0\t2\t1"
## [67] "35\t1\t0.0\t2\t1"
## [68] "36\t10\t0.0\t2\t10"
## [69] "39\t1\t0.0\t2\t1"
## [70] "40\t1\t0.0\t2\t1"
## [71] "41\t1\t0.0\t2\t1"
## [72] "44\t1\t0.0\t2\t1"
## [73] "50\t1\t0.0\t2\t1"
## [74] "55\t1\t0.0\t2\t1"
## [75] "57\t2\t0.0\t2\t2"
## [76] "65\t1\t0.0\t2\t1"
## [77] "68\t12\t0.0\t2\t12"
## [78] "69\t4\t0.0\t2\t4"
## [79] "72\t1\t0.0\t2\t1"
## [80] "74\t1\t0.0\t2\t1"
## [81] "75\t1\t0.0\t2\t1"
## [82] "77\t2\t0.0\t2\t2"
## [83] "78\t1\t0.0\t2\t1"
## [84] "79\t1\t0.0\t2\t1"
## [85] "82\t3\t0.0\t2\t3"
## [86] "86\t1\t0.0\t2\t1"
## [87] "91\t1\t0.0\t2\t1"
## [88] "92\t2\t0.0\t2\t2"
## [89] "98\t1\t0.0\t2\t1"
## [90] "99\t1\t0.0\t2\t1"
## [91] "101\t1\t0.0\t2\t1"
## [92] "105\t1\t0.0\t2\t1"
## [93] "111\t1\t0.0\t2\t1"
## [94] "120\t1\t0.0\t2\t1"
## [95] "126\t1\t0.0\t2\t0 1"
## [96] "137\t1\t0.0\t2\t1"
## [97] "144\t1\t0.0\t2\t1"
## [98] "146\t1\t0.0\t2\t0 1"
## [99] ""
## [100] ""
## [101] "=== Second read: Adapter 3 ==="
## [102] ""
## [103] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 2 times"
## [104] ""
## [105] "No. of allowed errors:"
## [106] "0-9 bp: 0; 10-19 bp: 1; 20 bp: 2"
## [107] ""
## [108] "Overview of removed sequences"
## [109] "length\tcount\texpect\tmax.err\terror counts"
## [110] "17\t1\t0.0\t1\t1"
## [111] "125\t1\t0.0\t2\t1"
## [112] ""
## [113] ""
## [114] "=== Second read: Adapter 4 ==="
## [115] ""
## [116] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 346 times"
## [117] ""
## [118] "No. of allowed errors:"
## [119] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [120] ""
## [121] "Bases preceding removed adapters:"
## [122] " A: 96.0%"
## [123] " C: 2.6%"
## [124] " G: 0.3%"
## [125] " T: 1.2%"
## [126] " none/other: 0.0%"
## [127] "WARNING:"
## [128] " The adapter is preceded by \"A\" extremely often."
## [129] " The provided adapter sequence could be incomplete at its 3' end."
## [130] ""
## [131] "Overview of removed sequences"
## [132] "length\tcount\texpect\tmax.err\terror counts"
## [133] "5\t7\t8.8\t0\t7"
## [134] "7\t2\t0.6\t0\t2"
## [135] "9\t4\t0.0\t0\t4"
## [136] "10\t3\t0.0\t1\t3"
## [137] "11\t1\t0.0\t1\t1"
## [138] "12\t2\t0.0\t1\t1 1"
## [139] "13\t1\t0.0\t1\t1"
## [140] "14\t2\t0.0\t1\t1 1"
## [141] "16\t2\t0.0\t1\t2"
## [142] "17\t1\t0.0\t1\t1"
## [143] "19\t2\t0.0\t1\t2"
## [144] "20\t2\t0.0\t2\t2"
## [145] "21\t3\t0.0\t2\t3"
## [146] "22\t4\t0.0\t2\t3 1"
## [147] "25\t8\t0.0\t2\t7 1"
## [148] "26\t2\t0.0\t2\t1 1"
## [149] "27\t21\t0.0\t2\t17 3 1"
## [150] "28\t2\t0.0\t2\t1 1"
## [151] "29\t3\t0.0\t2\t2 0 1"
## [152] "30\t2\t0.0\t3\t1 1"
## [153] "31\t1\t0.0\t3\t1"
## [154] "32\t2\t0.0\t3\t2"
## [155] "33\t3\t0.0\t3\t2 0 1"
## [156] "34\t4\t0.0\t3\t3 1"
## [157] "35\t2\t0.0\t3\t1 1"
## [158] "36\t3\t0.0\t3\t1 2"
## [159] "37\t1\t0.0\t3\t1"
## [160] "38\t1\t0.0\t3\t0 1"
## [161] "39\t1\t0.0\t3\t1"
## [162] "40\t2\t0.0\t4\t2"
## [163] "42\t1\t0.0\t4\t1"
## [164] "43\t1\t0.0\t4\t0 0 1"
## [165] "44\t4\t0.0\t4\t0 1 1 1 1"
## [166] "46\t4\t0.0\t4\t3 1"
## [167] "47\t7\t0.0\t4\t4 0 2 1"
## [168] "48\t1\t0.0\t4\t0 1"
## [169] "49\t1\t0.0\t4\t1"
## [170] "50\t1\t0.0\t4\t1"
## [171] "51\t1\t0.0\t4\t1"
## [172] "52\t6\t0.0\t4\t3 1 2"
## [173] "53\t4\t0.0\t4\t3 0 1"
## [174] "55\t3\t0.0\t4\t1 2"
## [175] "56\t1\t0.0\t4\t1"
## [176] "58\t1\t0.0\t4\t1"
## [177] "59\t3\t0.0\t4\t3"
## [178] "60\t3\t0.0\t4\t3"
## [179] "61\t2\t0.0\t4\t2"
## [180] "63\t6\t0.0\t4\t6"
## [181] "64\t15\t0.0\t4\t11 3 1"
## [182] "65\t4\t0.0\t4\t2 1 0 0 1"
## [183] "66\t1\t0.0\t4\t0 1"
## [184] "67\t3\t0.0\t4\t2 1"
## [185] "68\t1\t0.0\t4\t1"
## [186] "69\t2\t0.0\t4\t1 0 0 1"
## [187] "70\t1\t0.0\t4\t1"
## [188] "71\t3\t0.0\t4\t3"
## [189] "72\t2\t0.0\t4\t2"
## [190] "73\t4\t0.0\t4\t4"
## [191] "74\t2\t0.0\t4\t2"
## [192] "75\t6\t0.0\t4\t5 1"
## [193] "76\t5\t0.0\t4\t5"
## [194] "77\t2\t0.0\t4\t2"
## [195] "78\t3\t0.0\t4\t3"
## [196] "79\t3\t0.0\t4\t3"
## [197] "80\t3\t0.0\t4\t2 1"
## [198] "83\t2\t0.0\t4\t1 1"
## [199] "84\t2\t0.0\t4\t1 1"
## [200] "85\t3\t0.0\t4\t3"
## [201] "86\t4\t0.0\t4\t4"
## [202] "87\t3\t0.0\t4\t2 1"
## [203] "89\t1\t0.0\t4\t1"
## [204] "91\t1\t0.0\t4\t1"
## [205] "92\t1\t0.0\t4\t1"
## [206] "93\t2\t0.0\t4\t2"
## [207] "94\t6\t0.0\t4\t6"
## [208] "95\t2\t0.0\t4\t2"
## [209] "96\t13\t0.0\t4\t13"
## [210] "97\t8\t0.0\t4\t8"
## [211] "99\t3\t0.0\t4\t1 2"
## [212] "101\t1\t0.0\t4\t1"
## [213] "102\t4\t0.0\t4\t4"
## [214] "103\t5\t0.0\t4\t5"
## [215] "104\t8\t0.0\t4\t8"
## [216] "105\t22\t0.0\t4\t18 3 1"
## [217] "106\t1\t0.0\t4\t1"
## [218] "107\t2\t0.0\t4\t2"
## [219] "108\t1\t0.0\t4\t1"
## [220] "110\t6\t0.0\t4\t6"
## [221] "111\t2\t0.0\t4\t2"
## [222] "113\t1\t0.0\t4\t1"
## [223] "114\t1\t0.0\t4\t1"
## [224] "115\t3\t0.0\t4\t3"
## [225] "118\t1\t0.0\t4\t0 0 0 1"
## [226] "119\t1\t0.0\t4\t1"
## [227] "120\t3\t0.0\t4\t1 2"
## [228] "121\t1\t0.0\t4\t0 1"
## [229] "122\t2\t0.0\t4\t2"
## [230] "124\t1\t0.0\t4\t1"
## [231] "126\t3\t0.0\t4\t3"
## [232] "127\t1\t0.0\t4\t1"
## [233] "128\t2\t0.0\t4\t2"
## [234] "129\t1\t0.0\t4\t1"
## [235] "133\t2\t0.0\t4\t2"
## [236] "135\t1\t0.0\t4\t1"
## [237] "136\t2\t0.0\t4\t2"
## [238] "138\t1\t0.0\t4\t1"
## [239] "139\t2\t0.0\t4\t2"
## [240] "140\t1\t0.0\t4\t1"
## [241] "146\t1\t0.0\t4\t1"
## [242] "148\t1\t0.0\t4\t1"
## [243] "152\t1\t0.0\t4\t1"
## [244] "154\t1\t0.0\t4\t1"
## [245] "162\t1\t0.0\t4\t1"
## [246] "165\t2\t0.0\t4\t2"
## [247] "172\t1\t0.0\t4\t1"
## [248] "174\t1\t0.0\t4\t1"
## [249] ""
## [250] ""
## [251] "WARNING:"
## [252] " One or more of your adapter sequences may be incomplete."
## [253] " Please see the detailed output above."
##
## [[68]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/BA1RNA1_S68_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/BA1RNA1_S68_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/BA1RNA1_S68_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/BA1RNA1_S68_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.03 s (157 us/read; 0.38 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 189"
## [9] " Read 1 with adapter: 0 (0.0%)"
## [10] " Read 2 with adapter: 6 (3.2%)"
## [11] "Pairs written (passing filters): 189 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 79,380 bp"
## [14] " Read 1: 37,044 bp"
## [15] " Read 2: 42,336 bp"
## [16] "Total written (filtered): 79,007 bp (99.5%)"
## [17] " Read 1: 37,044 bp"
## [18] " Read 2: 41,963 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 0 times"
## [27] ""
## [28] "=== Second read: Adapter 3 ==="
## [29] ""
## [30] "Sequence: CCGYCAATTYMTTTRAGTTT; Type: regular 5'; Length: 20; Trimmed: 0 times"
## [31] ""
## [32] "=== Second read: Adapter 4 ==="
## [33] ""
## [34] "Sequence: TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG; Type: regular 3'; Length: 40; Trimmed: 6 times"
## [35] ""
## [36] "No. of allowed errors:"
## [37] "0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40 bp: 4"
## [38] ""
## [39] "Bases preceding removed adapters:"
## [40] " A: 83.3%"
## [41] " C: 0.0%"
## [42] " G: 16.7%"
## [43] " T: 0.0%"
## [44] " none/other: 0.0%"
## [45] ""
## [46] "Overview of removed sequences"
## [47] "length\tcount\texpect\tmax.err\terror counts"
## [48] "16\t1\t0.0\t1\t1"
## [49] "34\t1\t0.0\t3\t1"
## [50] "66\t1\t0.0\t4\t1"
## [51] "69\t1\t0.0\t4\t0 1"
## [52] "85\t1\t0.0\t4\t1"
## [53] "103\t1\t0.0\t4\t1"
##
## [[69]]
## [1] "This is cutadapt 2.10 with Python 3.6.5"
## [2] "Command line parameters: -g CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA -a AAACTYAAAKRAATTGRCGG -G CCGYCAATTYMTTTRAGTTT -A TTACCGCGGCKGCTGRCACGGACTGGCCGTCGTTTTACGG --overlap 5 --minimum-length 50 -n 2 -o /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered_and_cut/BA1RNA2_S69_L001_R1_001.fastq.gz -p /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered_and_cut/BA1RNA2_S69_L001_R2_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_F/filtered/BA1RNA2_S69_L001_R1_001.fastq.gz /Users/melo.d/Desktop/Research/Oman_fieldwork/Samail_16S_compilation_fq_outputs/2017/02_filter/preprocessed_R/filtered/BA1RNA2_S69_L001_R2_001.fastq.gz"
## [3] "Processing reads on 1 core in paired-end mode ..."
## [4] "Finished in 0.08 s (137 us/read; 0.44 M reads/minute)."
## [5] ""
## [6] "=== Summary ==="
## [7] ""
## [8] "Total read pairs processed: 603"
## [9] " Read 1 with adapter: 16 (2.7%)"
## [10] " Read 2 with adapter: 37 (6.1%)"
## [11] "Pairs written (passing filters): 603 (100.0%)"
## [12] ""
## [13] "Total basepairs processed: 253,260 bp"
## [14] " Read 1: 118,188 bp"
## [15] " Read 2: 135,072 bp"
## [16] "Total written (filtered): 248,388 bp (98.1%)"
## [17] " Read 1: 116,641 bp"
## [18] " Read 2: 131,747 bp"
## [19] ""
## [20] "=== First read: Adapter 1 ==="
## [21] ""
## [22] "Sequence: CCGTAAAACGACGGCCAGTCCGTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 40; Trimmed: 0 times"
## [23] ""
## [24] "=== First read: Adapter 2 ==="
## [25] ""
## [26] "Sequence: AAACTYAAAKRAATTGRCGG; Type: regular 3'; Length: 20; Trimmed: 16 times"
## [27] ""
## [28] "No. of allowed errors:"